RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9085
(394 letters)
>gnl|CDD|163700 cd08069, MPN_RPN11_CSN5, Mov34/MPN/PAD-1 family: proteasomal
regulatory protein Rpn11 and signalosome complex subunit
CSN5. This family contains proteasomal regulatory
protein Rpn11 (26S proteasome regulatory subunit rpn11;
PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the
19S-proteasome; regulatory particle number 11) and
signalosomal CSN5 (COP9 signalosome complex subunit 5;
COP9 complex homolog subunit 5; c-Jun activation
domain-binding protein-1; CSN5/JAB1; JAB1). COP9
signalosome (CSN) and the proteasome lid are paralogous
complexes and their respective subunits CSN5 and Rpn11
are most closely related between the two complexes, both
containing the conserved JAMM (JAB1/MPN/Mov34
metalloenzyme) motif involved in zinc ion coordination
and providing the active site for isopeptidase activity.
Rpn11 is responsible for substrate deubiquitination
during proteasomal degradation. It is essential for
maintaining a correct cell cycle and normal
mitochondrial morphology and physiology; mutations in
Rpn11 cause cell cycle and mitochondrial defects,
temperature sensitivity and sensitivity to DNA damaging
reagents such as UV. It has been shown that the
C-terminal region of Rpn11 is involved in the regulation
of the mitochondrial fission and tubulation processes.
CSN5, one of the eight subunits of CSN, is critical for
nuclear export and the degradation of several tumor
suppressor proteins, including p53, p27, and Smad4. Its
MPN+ domain is critical for the physical interaction of
RUNX3 and Jab1. It has been suggested that the direct
interaction of CSN5/JAB1 with p27 provides p27 with a
leucine-rich nuclear export signal (NES), which is
required for binding to chromosomal region maintenance 1
(CRM1), and facilitates nuclear export. The
over-expression of CSN5/JAB1 also has been implicated in
cancer initiation and progression, including cancer of
the lung, pancreas, mouth, thyroid, and breast,
suggesting that the oncogenic activity of CSN5 is
associated with the down-regulation of RUNX3.
Length = 268
Score = 429 bits (1105), Expect = e-152
Identities = 158/271 (58%), Positives = 197/271 (72%), Gaps = 7/271 (2%)
Query: 97 PWEKDPHFFKDIKISALALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGT 156
PW+ DP +F+ + IS+LALLKM+ HAR+GG +EVMGL+LGK+D ++IV+D FALPVEGT
Sbjct: 1 PWKPDPDYFEKVYISSLALLKMLKHARAGGPIEVMGLMLGKVDDYTIIVVDVFALPVEGT 60
Query: 157 ETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQE 216
ETRVNAQ + EYM Y E K+ GR EN +GWYHSHPGYGCWLSGIDV+TQ LNQ Q+
Sbjct: 61 ETRVNAQDEFQEYMVQY-EMLKQTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQD 119
Query: 217 PFVAIVIDPVRTISAGKVCLGSFRTYPKGYKP--ANEEPSEYQTIPLNKIEDFGVHCKQY 274
PFVA+V+DP+R++ GKV +G+FRT P GYKP + S +P KIEDFG H KQY
Sbjct: 120 PFVAVVVDPIRSLVKGKVVIGAFRTIPPGYKPLEPRQTTSNIGHLPKPKIEDFGGHNKQY 179
Query: 275 YSLDVSYFKSSLDRRLLDSLWNKYWVNTLSSSSLLTNA-DYLTGQMCDLSDKLEQAESAL 333
YSL + YFKSSLDR+LL +LWNKYWVNTLS S LL N+ +Y Q+ DL++KLE+AE
Sbjct: 180 YSLPIEYFKSSLDRKLLLNLWNKYWVNTLSLSPLLENSNEYTIKQILDLAEKLEKAEQQE 239
Query: 334 VRNFLISESQERRPETKLMKATKDCCKTTIE 364
R L E + KL KA +D K +E
Sbjct: 240 ER--LTGEELDIANVGKLDKA-RDSSKIHLE 267
>gnl|CDD|216478 pfam01398, JAB, JAB1/Mov34/MPN/PAD-1 ubiquitin protease. Members
of this family are found in proteasome regulatory
subunits, eukaryotic initiation factor 3 (eIF3) subunits
and regulators of transcription factors. This family is
also known as the MPN domain and PAD-1-like domain,
JABP1 domain or JAMM domain. These are metalloenzymes
that function as the ubiquitin isopeptidase/
deubiquitinase in the ubiquitin-based signaling and
protein turnover pathways in eukaryotes. Versions of the
domain in prokaryotic cognates of the
ubiquitin-modification pathway are predicted to have a
similar role.
Length = 117
Score = 137 bits (346), Expect = 1e-39
Identities = 56/113 (49%), Positives = 70/113 (61%), Gaps = 3/113 (2%)
Query: 108 IKISALALLKMVMHARSGGTL--EVMGLLLGKIDANSMI-VMDAFALPVEGTETRVNAQA 164
+ I L LLK+V HAR GG EVMG+LLG ++ + +I V ++FALP TE V A
Sbjct: 5 VVIHPLVLLKIVDHARRGGKSGEEVMGVLLGTLEGDRVIEVTNSFALPQSETEDDVEAVE 64
Query: 165 QAYEYMTAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEP 217
+EYM +E K+V R E +GWYHSHPGYGCWLS +DV TQ L Q
Sbjct: 65 LDHEYMEKMLEMLKKVNRDEEVVGWYHSHPGYGCWLSSVDVHTQELYQRMIPE 117
>gnl|CDD|214573 smart00232, JAB_MPN, JAB/MPN domain. Domain in Jun kinase
activation domain binding protein and proteasomal
subunits. Domain at Mpr1p and Pad1p N-termini. Domain of
unknown function.
Length = 135
Score = 131 bits (331), Expect = 3e-37
Identities = 44/137 (32%), Positives = 71/137 (51%), Gaps = 3/137 (2%)
Query: 108 IKISALALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAY 167
+K+ L L ++ HA G EV G+LLGK + + V + FA+P E + V Q
Sbjct: 2 VKVHPLVPLNILKHAIRDGPEEVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSV--QEYDE 59
Query: 168 EYMTAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVR 227
+Y E K+V + +GWYHSHP + S +DV+T Q V +++DP++
Sbjct: 60 DYSHLMDEELKKVNKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIK 119
Query: 228 TISAGKVCLGSFRTYPK 244
+ G++ L +FR P+
Sbjct: 120 SFQ-GRLSLRAFRLTPE 135
>gnl|CDD|163689 cd08058, MPN_euk_mb, Mpr1p, Pad1p N-terminal (MPN) domains with
catalytic isopeptidase activity (metal-binding);
eukaryotic. This family contains eukaryotic MPN (also
known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in
proteins with a variety of functions, including AMSH
(associated molecule with the Src homology 3 domain
(SH3) of STAM), H2A-DUB (histone H2A deubiquitinase),
BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as
well as Rpn11 (regulatory particle number 11) and CSN5
(COP9 signalosome complex subunit 5). These domains
contain the signature JAB1/MPN/Mov34 metalloenzyme
(JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc
ion coordination and provides the active site for
isopeptidase activity. Rpn11 is responsible for
substrate deubiquitination during proteasomal
degradation. It is essential for maintaining a correct
cell cycle and normal mitochondrial morphology and
physiology. CSN5 is critical for nuclear export and the
degradation of several tumor suppressor proteins,
including p53, p27, and Smad4. Over-expression of CSN5
has been implicated in cancer initiation and
progression. AMSH specifically cleaves Lys 63 and not
Lys48-linked polyubiquitin (poly-Ub) chains, thus
facilitating the recycling and subsequent trafficking of
receptors to the cell surface. It is involved in the
degradation of EGF receptor (EGFR) and possibly other
ubiquitinated endocytosed proteins. BRCC36 is part of
the BRCA1/BRCA2/BARD1-containing nuclear complex that
displays an E3 ubiquitin ligase activity; it is targeted
to DNA damage foci after irradiation. 2A-DUB is specific
for monoubiquitinated H2A (uH2A), regulating
transcription by coordinating histone acetylation and
deubiquitination, and destabilizing the association of
linker histone H1 with nucleosomes. It is a positive
regulator of androgen receptor (AR) transactivation
activity on a reporter gene and serves as a marker in
prostate tumors.
Length = 119
Score = 94.6 bits (235), Expect = 1e-23
Identities = 45/133 (33%), Positives = 58/133 (43%), Gaps = 21/133 (15%)
Query: 113 LALLKMVMHARSGGTLEVMGLLLGKIDANS-----MIVMDAFALPVEGTETRVNAQAQAY 167
ALLKM+ HA S +EVMGLL G++ N +IV A P T + +
Sbjct: 1 DALLKMLQHAESNTGIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCTGEN---VEELF 57
Query: 168 EYMTAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVR 227
T GR +GWYHSHP + WLS +D+ TQ Q +AIV+ P
Sbjct: 58 NVQT---------GRPLLVVGWYHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKH 108
Query: 228 TISAGKVCLGSFR 240
G FR
Sbjct: 109 R----NKDTGIFR 117
>gnl|CDD|224229 COG1310, COG1310, Predicted metal-dependent protease of the
PAD1/JAB1 superfamily [General function prediction
only].
Length = 134
Score = 76.4 bits (188), Expect = 7e-17
Identities = 34/120 (28%), Positives = 45/120 (37%), Gaps = 12/120 (10%)
Query: 108 IKISALALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAY 167
+ I L ++ HAR EV GLL G + F L E V
Sbjct: 2 LVIPKEVLGAILEHARREHPREVCGLLAGTRE-----GERYFPLKNVSVE-PVEYFEIDP 55
Query: 168 EYMTAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVR 227
EY Y+ A E +GWYHSHPG + S D L P++ + + P R
Sbjct: 56 EYSLFYLAAEDAG---EVVVGWYHSHPGGPPYPSEADRRLSKLGPL---PWLIVSVPPGR 109
>gnl|CDD|163699 cd08068, MPN_BRCC36, Mov34/MPN/PAD-1 family: BRCC36, a subunit of
BRCA1-A complex. BRCC36 (BRCA1-A complex subunit
BRCC36; BRCA1/BRCA2-containing complex subunit 36;
BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC
complex subunit BRCC36; BRCC36 isopeptidase complex;
Lys-63-specific deubiquitinase BRCC36) and BRCC36-like
domains are members of JAMM/MPN+ deubiquitinases (DUBs),
possibly with Zn2+-dependent ubiquitin isopeptidase
activity. BRCC36 is part of the
BRCA1/BRCA2/BARD1-containing nuclear complex that
displays an E3 ubiquitin ligase activity. It is targeted
to DNA damage foci after irradiation; RAP80 recruits the
Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand
breaks (DSBs) for DNA repair through specific
recognition of Lys 63-linked polyubiquitinated proteins
by its tandem ubiquitin-interacting motifs. A new
protein, MERIT40 (mediator of RAP80 interactions and
targeting 40 kDa), also named NBA1 (new component of the
BRCA1 A complex), exists in the same BRCA1-containing
complex and is essential for the integrity of the
complex. There are studies suggesting that MERIT40/NBA1
ties BRCA1 complex integrity, DSB recognition, and
ubiquitin chain activities to the DNA damage response.
It has also been shown that BRCA1-containing complex
resembles the lid complex of the 26S proteasome.
Length = 244
Score = 70.1 bits (172), Expect = 9e-14
Identities = 42/133 (31%), Positives = 57/133 (42%), Gaps = 23/133 (17%)
Query: 106 KDIKISALALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFA-------LP------ 152
+ +SA L + HA S EVMGLL+G+I+ + A L
Sbjct: 2 SKVHLSADVYLVCLTHALSTEKEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRK 61
Query: 153 --VE-GTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQM 209
VE E A +A E +T +E GR +GWYHSHP W S +DV TQ
Sbjct: 62 DRVEISPEQLSAASTEA-ERLT------EETGRPMRVVGWYHSHPHITVWPSHVDVRTQA 114
Query: 210 LNQNFQEPFVAIV 222
+ Q FV ++
Sbjct: 115 MYQMMDSGFVGLI 127
>gnl|CDD|163698 cd08067, MPN_2A_DUB, Mov34/MPN/PAD-1 family: Histone H2A
deubiquitinase. This family includes histone H2A
deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM
and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or
KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases
(DUBs), with possible Zn2+-dependent ubiquitin
isopeptidase activity. It contains the SWIRM (Swi3p,
Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR,
TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain
can bind directly to DNA. 2A-DUB is specific for
monoubiquitinated H2A (uH2A), regulating transcription
by coordinating histone acetylation and
deubiquitination, and destabilizing the association of
linker histone H1 with nucleosomes. 2A-DUB interacts
with p/CAF (p300/CBP-associated factor) in a
co-regulatory protein complex, where the status of
acetylation of nucleosomal histones modulates its
deubiquitinase activity. 2A-DUB is a positive regulator
of androgen receptor (AR) transactivation activity on a
reporter gene; it participates in transcriptional
regulation events in androgen receptor-dependent gene
activation. In prostate tumors, the levels of uH2A are
dramatically decreased, thus 2A-DUB serving as a
cancer-related marker.
Length = 187
Score = 63.4 bits (155), Expect = 6e-12
Identities = 35/131 (26%), Positives = 54/131 (41%), Gaps = 23/131 (17%)
Query: 108 IKISALALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNA----- 162
+ +S+ ALL M H T EV+G L G D N+ + A P T ++
Sbjct: 7 VTVSSNALLLMDFHCHLT-TSEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEMDPV 65
Query: 163 -QAQAYEYMTAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNF------- 214
+ + E + + R + +GWYHSHP + S D+ TQ+ Q
Sbjct: 66 SETEIRESLES---------RGLSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSG 116
Query: 215 QEPFVAIVIDP 225
EP V ++ P
Sbjct: 117 YEPCVGLICSP 127
>gnl|CDD|163696 cd08065, MPN_eIF3h, Mpr1p, Pad1p N-terminal (MPN) domains without
catalytic isopeptidase activity, found in eIF2h.
Eukaryotic translation initiation factor 3 (eIF3)
subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma;
eIF3-p40) is an evolutionarily non-conserved subunit of
the functional core that comprises eIF3a, eIF3b, eIF3c,
eIF3e, eIF3f, and eIF3h, and contains the MPN domain.
However, it lacks the canonical JAMM motif, and
therefore does not show catalytic isopeptidase
activity.Together with eIF3e and eIF3f, eIF3h stabilizes
the eIF3 complex. Results suggest that eIF3h regulates
cell growth and viability, and that over-expression of
the gene may provide growth advantage to prostate,
breast, and liver cancer cells. For example, EIF3h gene
amplification is common in late-stage prostate cancer
suggesting that it may be functionally involved in the
progression of the disease. It has been shown that
coamplification of MYC, a well characterized oncogene
involved in cell growth, differentiation, and apoptosis,
and EIF3h in patients with non-small cell lung cancer
(NSCLC) improves survival if treated with the Epidermal
Growth Factor Receptor Tyrosine Kinase Inhibitor
(EGFR-TKI), Gefitinib. Plant eIF3h is implicated in
translation of specific mRNAs.
Length = 266
Score = 63.8 bits (156), Expect = 1e-11
Identities = 36/133 (27%), Positives = 58/133 (43%), Gaps = 2/133 (1%)
Query: 108 IKISALALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAY 167
++I L +LK++ H + V G LLG ++ V + F P + A
Sbjct: 3 VQIDGLVVLKIIKHCKEELPELVQGQLLGLDVGGTLEVTNCFPFPKSEEDDSDRADEDIA 62
Query: 168 EYMTAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDPVR 227
+Y + +EV N +GWY S G + + + TQ Q E V +V DP +
Sbjct: 63 DYQLEMMRLLREVNVDHNHVGWYQSTYL-GSFFTRDLIETQYNYQEAIEESVVLVYDPSK 121
Query: 228 TISAGKVCLGSFR 240
T S G + L ++R
Sbjct: 122 T-SQGSLSLKAYR 133
>gnl|CDD|163688 cd08057, MPN_euk_non_mb, Mpr1p, Pad1p N-terminal (MPN) domains
without catalytic isopeptidase activity (non
metal-binding); eukaryotic. This family contains MPN
(also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains
variants lacking key residues in the JAB1/MPN/Mov34
metalloenzyme (JAMM) motif and are unable to coordinate
a metal ion. Comparisons of key catalytic and metal
binding residues explain why the MPN-containing proteins
Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation
initiation factor 3 subunits f and h do not show
catalytic isopeptidase activity. It has been proposed
that the MPN domain in these proteins has a primarily
structural function. Rpn7 is known to be critical for
the integrity of the 26S proteasome complex by
establishing a correct lid structure. It is necessary
for the incorporation/anchoring of Rpn3 and Rpn12 to the
lid and essential for viability and normal mitosis. CSN6
is a highly conserved protein complex with diverse
functions, including several important intracellular
pathways such as the ubiquitin/proteasome system, DNA
repair, cell cycle, developmental changes, and some
aspects of immune responses. It cleaves ubiquitin-like
protein Nedd8 (neural precursor cell expressed,
developmentally downregulated 8)) in the cullin 1 in
cells. EIF3f s a potent inhibitor of HIV-1 replication
as well as an important negative regulator of cell
growth and proliferation. EIF3h regulates cell growth
and viability, and that over-expression of the gene may
provide growth advantage to prostate, breast, and liver
cancer cells.
Length = 157
Score = 55.9 bits (135), Expect = 2e-09
Identities = 32/153 (20%), Positives = 64/153 (41%), Gaps = 8/153 (5%)
Query: 108 IKISALALLKMV-MHARSGGTLE-VMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQ 165
+++ L LL + + R ++ V+G+LLG +D + + V ++F LP + E + +
Sbjct: 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVDGDKIEVTNSFELPFDEEEESIFIDTE 60
Query: 166 AYEYMTAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVS--TQMLNQNFQEPFVAIVI 223
E K+V E +GWY +S D S +Q + E + +++
Sbjct: 61 YLEKRYNLH---KKVYPQEKIVGWYSIGSNNSNEISKSDNSLHSQFSLISE-ENPLILIL 116
Query: 224 DPVRTISAGKVCLGSFRTYPKGYKPANEEPSEY 256
DP + K+ + +F + + A
Sbjct: 117 DPSLQSDSEKLEISTFTSAQREENGAEITYEIG 149
>gnl|CDD|222766 pfam14464, Prok-JAB, Prokaryotic homologs of the JAB domain. These
are metalloenzymes that function as the ubiquitin
isopeptidase/ deubiquitinase in the ubiquitin-based
signaling and protein turnover pathways in eukaryotes.
Prokaryotic JAB domains are predicted to have a similar
role in their cognates of the ubiquitin modification
pathway. The domain is widely found in bacteria, archaea
and phages where they are present in several gene
contexts in addition to those that correspond to the
prokaryotic cognates of the eukaryotic Ub pathway. Other
contexts in which JAB domains are present include gene
neighbor associations with ubiquitin fold domains in
cysteine and siderophore biosynthesis, and phage tail
morphogenesis, where they are shown or predicted to
process the associated ubiquitin. A distinct family, the
RadC-like JAB domains are widespread in bacteria and are
predicted to function as nucleases. In halophilic
archaea the JAB domain shows strong gene-neighborhood
associations with a nucleotidyltransferase suggesting a
role in nucleotide metabolism.
Length = 98
Score = 44.7 bits (106), Expect = 3e-06
Identities = 25/113 (22%), Positives = 37/113 (32%), Gaps = 20/113 (17%)
Query: 111 SALALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYM 170
L ++ HAR E GLL+G V+ AL E
Sbjct: 1 PESLLEAILAHARRAYPNEACGLLVGTERGERTRVVPLLALDPE-------DSFA----A 49
Query: 171 TAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVI 223
A + L +G YHSHPG + S D + + + I++
Sbjct: 50 AREDAARERGLEL---VGIYHSHPGGPAYPSETD------RRLARPLALYIIV 93
>gnl|CDD|163686 cd07767, MPN, Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also
known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are
found in the N-terminal termini of proteins with a
variety of functions; they are components of the
proteasome regulatory subunits, the signalosome (CSN),
eukaryotic translation initiation factor 3 (eIF3)
complexes, and regulators of transcription factors.
These domains are isopeptidases that release ubiquitin
from ubiquitinated proteins (thus having
deubiquitinating (DUB) activity) that are tagged for
degradation. Catalytically active MPN domains contain a
metalloprotease signature known as the JAB1/MPN/Mov34
metalloenzyme (JAMM) motif. For example, Rpn11 (also
known as POH1 or PSMD14), a subunit of the 19S
proteasome lid is involved in the ATP-dependent
degradation of ubiquitinated proteins, contains the
conserved JAMM motif involved in zinc ion coordination.
Poh1 is a regulator of c-Jun, an important regulator of
cell proliferation, differentiation, survival and death.
JAB1 is a component of the COP9 signalosome (CSN), a
regulatory particle of the ubiquitin (Ub)/26S proteasome
system occurring in all eukaryotic cells; it cleaves the
ubiquitin-like protein NEDD8 from the cullin subunit of
the SCF (Skp1, Cullins, F-box proteins) family of E3
ubiquitin ligases. AMSH (associated molecule with the
SH3 domain of STAM, also known as STAMBP), a member of
JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves
Lys 63-linked polyubiquitin (poly-Ub) chains, thus
facilitating the recycling and subsequent trafficking of
receptors to the cell surface. Similarly, BRCC36, part
of the nuclear complex that includes BRCA1 protein and
is targeted to DNA damage foci after irradiation,
specifically disassembles K63-linked polyUb. BRCC36 is
aberrantly expressed in sporadic breast tumors,
indicative of a potential role in the pathogenesis of
the disease. Some variants of the JAB1/MPN domains lack
key residues in their JAMM motif and are unable to
coordinate a metal ion. Comparisons of key catalytic and
metal binding residues explain why the MPN-containing
proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the
translation initiation factor 3 subunits f (p47) and h
(p40) do not show catalytic isopeptidase activity. It
has been proposed that the MPN domain in these proteins
has a primarily structural function.
Length = 116
Score = 43.7 bits (103), Expect = 1e-05
Identities = 31/111 (27%), Positives = 49/111 (44%), Gaps = 7/111 (6%)
Query: 115 LLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYI 174
L + A+S EV+GLL G + V + A+P + + N Y
Sbjct: 1 LKMFLDAAKSINGKEVIGLLYGSKTKKVLDVDEVIAVPFDEGDKDDNVWFLMYLDF---- 56
Query: 175 EAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPFVAIVIDP 225
K++ +GWYH+HP C+LS D++T L Q + V I++D
Sbjct: 57 ---KKLNAGLRIVGWYHTHPKPSCFLSPNDLATHELFQRYFPEKVMIIVDV 104
>gnl|CDD|163701 cd08070, MPN_like, Mpr1p, Pad1p N-terminal (MPN) domains with
catalytic isopeptidase activity (metal-binding). This
family contains archaeal and bacterial MPN (also known
as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These
domains contain the signature JAB1/MPN/Mov34
metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is
involved in zinc ion coordination and provides the
active site for isopeptidase activity for the release of
ubiquitin from ubiquitinated proteins (thus having
deubiquitinating (DUB) activity) that are tagged for
degradation. The JAMM proteins likely hydrolyze
ubiquitin conjugates in a manner similar to thermolysin,
in which the zinc-polarized aqua ligand serves as the
nucleophile, compared with the classical DUBs that do so
with a cysteine residue in the active site.
Length = 128
Score = 40.3 bits (95), Expect = 2e-04
Identities = 27/96 (28%), Positives = 40/96 (41%), Gaps = 11/96 (11%)
Query: 114 ALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALP--VEGTETR--VNAQAQAYEY 169
L ++ HA + E GLLLGK + IV + + + E R ++ E
Sbjct: 3 LLEAILAHAEAEYPEECCGLLLGKGGGVTAIVTEVYPVRNVAESPRRRFEIDPA----EQ 58
Query: 170 MTAYIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDV 205
+ A A+E G +G YHSHP S D+
Sbjct: 59 LAA-QREARERG--LEVVGIYHSHPDGPARPSETDL 91
>gnl|CDD|217666 pfam03665, UPF0172, Uncharacterized protein family (UPF0172). In
Chlamydomonas reinhardtii the protein TLA1 (truncated
light-harvesting chlorophyll antenna size) apparently
regulates genes that define the chlorophyll-a antenna
size in the photosynthetic apparatus. This family was
formerly known as UPF0172.
Length = 195
Score = 38.8 bits (91), Expect = 0.002
Identities = 16/39 (41%), Positives = 24/39 (61%)
Query: 107 DIKISALALLKMVMHARSGGTLEVMGLLLGKIDANSMIV 145
+++IS LA KM++HA V GLLLGK +S ++
Sbjct: 3 EVEISPLAYAKMILHAAKYPHCAVNGLLLGKSTKSSSVL 41
>gnl|CDD|163697 cd08066, MPN_AMSH_like, Mov34/MPN/PAD-1 family. AMSH (associated
molecule with the Src homology 3 domain (SH3) of STAM
(signal-transducing adapter molecule, also known as
STAMBP)) and AMSH-like proteins (AMSH-LP) are members of
JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent
ubiquitin isopeptidase activity. AMSH specifically
cleaves Lys 63 and not Lys48-linked polyubiquitin
(poly-Ub) chains, thus facilitating the recycling and
subsequent trafficking of receptors to the cell surface.
AMSH and AMSH-LP are anchored on the early endosomal
membrane via interaction with the clathrin coat. AMSH
shares a common SH3-binding site with another endosomal
DUB, UBPY (ubiquitin-specific protease Y; also known as
USP8), the latter being a cysteine protease that does
not discriminate between Lys48 and Lys63-linked
ubiquitin. AMSH is involved in the degradation of EGF
receptor (EGFR) and possibly other ubiquitinated
endocytosed proteins. AMSH also interacts with CHMP1,
CHMP2, and CHMP3 proteins, all of which are components
of ESCRT-III, suggested to be required for EGFR
down-regulation. The function of AMSH-LP has not been
elucidated; however, it exhibits two fundamentally
distinct features from AMSH: first, there is a
substitution in the critical amino acid residue in the
SH3-binding motif (SBM) in the human AMSH-LP, but not in
its mouse ortholog, and lacks STAM-binding ability;
second, AMSH-LP lacks the ability to interact with CHMP
proteins. It is therefore likely that AMSH and AMSH-LP
play different roles on early endosomes.
Length = 173
Score = 37.6 bits (88), Expect = 0.004
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 10/44 (22%)
Query: 187 IGWYHSHPGYGCWLSGIDVSTQ-----MLNQNFQEPFVAIVIDP 225
+GW H+HP C+LS +D+ T ML + +AIV P
Sbjct: 78 LGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEA-----IAIVCAP 116
>gnl|CDD|163691 cd08060, MPN_UPF0172, Mov34/MPN/PAD-1 family: UPF0172 family of
unknown function includes neighbor of COX4 (Noc4p).
This family includes Noc4p (neighbor of COX4; neighbor
of Cytochrome c Oxidase 4; nucleolar complex associated
4 homolog) which belongs to the family of unknown
function, UPF0172, with MPN/JAMM-like domains. Proteins
in this family are homologs of the NOC4 gene which is
conserved in eukaryotic members including human, dog,
mouse, rat, chicken, zebrafish, fruit fly, mosquito,
S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa,
A.thaliana, and rice. NOC4 highly expressed in the
pancreas and moderately in liver, heart, lung, kidney,
brain, skeletal muscle, and placenta. This nucleolar
protein forms a complex with Nop14p that mediates
maturation and nuclear export of 40S ribosomal subunits.
This family of eukaryotic MPN-like domains lacks the key
residues that coordinate a metal ion and therefore does
not show catalytic isopeptidase activity.
Length = 182
Score = 37.7 bits (88), Expect = 0.005
Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 110 ISALALLKMVMHARSGGTLEVMGLLLGKIDAN-SMIVMDAFAL 151
+S LA +KM++HA V GLLLGK + S+ + DA L
Sbjct: 1 LSTLAYVKMLLHAAKYPHCAVNGLLLGKKSSGGSVEITDAVPL 43
>gnl|CDD|163690 cd08059, MPN_prok_mb, Mpr1p, Pad1p N-terminal (MPN) domains with
catalytic isopeptidase activity (metal-binding);
prokaryotic. This family contains bacterial and
archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB,
MPN+)-like domains. These catalytically active domains
contain the signature JAB1/MPN/Mov34 metalloenzyme
(JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc
ion coordination and provides the active site for
isopeptidase activity for the release of ubiquitin from
ubiquitinated proteins (thus having deubiquitinating
(DUB) activity) that are tagged for degradation. The
JAMM proteins likely hydrolyze ubiquitin conjugates in a
manner similar to thermolysin, in which the
zinc-polarized aqua ligand serves as the nucleophile,
compared with the classical DUBs that do so with a
cysteine residue in the active site.
Length = 101
Score = 35.2 bits (81), Expect = 0.009
Identities = 22/91 (24%), Positives = 33/91 (36%), Gaps = 16/91 (17%)
Query: 118 MVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAA 177
+++HA+ E G L G D VMD + + + A +E
Sbjct: 6 ILVHAKDAHPDEFCGFLSGSKDN----VMDELIFLPFVSGS------VSAVIDLAALEIG 55
Query: 178 KEVGRLENAIGWYHSHPGYGCWLSGIDVSTQ 208
+V +G HSHP C S D+S
Sbjct: 56 MKV------VGLVHSHPSGSCRPSEADLSLF 80
>gnl|CDD|201631 pfam01158, Ribosomal_L36e, Ribosomal protein L36e.
Length = 95
Score = 34.1 bits (79), Expect = 0.019
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 12/38 (31%)
Query: 6 ELAVGLKKGHRNTKIKWANSLAQKTSKIVKMRPSRLKG 43
+AVGL KGH+ TK + K RPSR KG
Sbjct: 1 GIAVGLNKGHKVTK------------RPRKPRPSRRKG 26
>gnl|CDD|163695 cd08064, MPN_eIF3f, Mpr1p, Pad1p N-terminal (MPN) domains without
catalytic isopeptidase activity, found in eIF3f.
Eukaryotic translation initiation factor 3 (eIF3)
subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic
translation initiation factor 3, subunit 5 epsilon,
47kDa; Mov34/MPN/PAD-1 family protein) is an
evolutionarily non-conserved subunit of the functional
core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f,
and eIF3h, and contains the MPN domain. However, it
lacks the canonical JAMM motif, and therefore does not
show catalytic isopeptidase activity. It has been shown
that eIF3f mRNA expression is significantly decreased in
many human tumors including pancreatic cancer and
melanoma. EIF3f is a potent inhibitor of HIV-1
replication; it mediates restriction of HIV-1 expression
through several factors including the
serine/arginine-rich (SR) protein 9G8, and
cyclin-dependent kinase 11 (CDK11). EIF3f
phosphorylation by CDK11 is important in regulating its
function in translation and apoptosis. It enhances its
association with the core eIF3 subunits during
apoptosis, suggesting that eIF3f may inhibit translation
by increasing the binding to the eIF3 complex during
apoptosis. Thus, eIF3f may be an important negative
regulator of cell growth and proliferation.
Length = 265
Score = 34.1 bits (79), Expect = 0.095
Identities = 20/85 (23%), Positives = 39/85 (45%), Gaps = 5/85 (5%)
Query: 108 IKISALALLKMVMHA--RSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQ 165
+++ + L ++ R+ G V+G LLG + + + FA+P +E +V +
Sbjct: 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNESEDQVAVDME 60
Query: 166 AYEYMTAYIEAAKEVGRLENAIGWY 190
+ M E ++V E +GWY
Sbjct: 61 YHRTM---YELHQKVNPKEVIVGWY 82
>gnl|CDD|215417 PLN02781, PLN02781, Probable caffeoyl-CoA O-methyltransferase.
Length = 234
Score = 32.9 bits (75), Expect = 0.22
Identities = 26/106 (24%), Positives = 50/106 (47%), Gaps = 20/106 (18%)
Query: 113 LALLKMVMHARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTA 172
L++L +M+A++ TLE+ G+ G ++ A ALP +G T ++ +AYE
Sbjct: 60 LSMLVKIMNAKN--TLEI-GVFTG-----YSLLTTALALPEDGRITAIDIDKEAYEVGLE 111
Query: 173 YIEAAKEVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQNFQEPF 218
+I+ A +++ I + S + Q+LN + + F
Sbjct: 112 FIKKAG----VDHKINFIQS--------DALSALDQLLNNDPKPEF 145
>gnl|CDD|163693 cd08062, MPN_RPN7_8, Mpr1p, Pad1p N-terminal (MPN) domains without
catalytic isopeptidase activity, found in 19S
proteasomal subunits Rpn7 and Rpn8. This family
includes lid subunits of the 26 S proteasome regulatory
particles, Rpn7 (PSMD7; proteasome 26S non-ATPase
subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S
non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be
critical for the integrity of the 26 S proteasome
complex by establishing a correct lid structure. It is
necessary for the incorporation/anchoring of Rpn3 and
Rpn12 to the lid and essential for viability and normal
mitosis. Rpn7 and Rpn8 are ATP-independent components of
the 19S regulator subunit, and contain the MPN
structural motif on its N-terminal region. However,
while they show a typical MPN metalloprotease fold, they
lack the canonical JAMM motif, and therefore do not show
catalytic isopeptidase activity. It is suggested that
Rpn7 function is primarily structural.
Length = 280
Score = 32.2 bits (74), Expect = 0.42
Identities = 25/85 (29%), Positives = 39/85 (45%), Gaps = 3/85 (3%)
Query: 113 LALLKMVMH---ARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEY 169
L LL +V H G + V+G+LLG + V ++FA+P E E + + Y
Sbjct: 8 LVLLSVVDHYNRVAKGTSKRVVGVLLGSWKKGVLDVTNSFAVPFEEDEKDPSVWFLDHNY 67
Query: 170 MTAYIEAAKEVGRLENAIGWYHSHP 194
+ K+V E +GWY + P
Sbjct: 68 LENMYGMFKKVNAKEKIVGWYSTGP 92
>gnl|CDD|218228 pfam04720, DUF506, Protein of unknown function (DUF506). Family of
uncharacterized plant proteins.
Length = 218
Score = 30.1 bits (68), Expect = 1.6
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 320 CDLSDKLEQAESALVRNFLISESQERRPETKLMKATK 356
D+SD+L+ L+ L E R E K+ +A +
Sbjct: 43 GDVSDELKS----LLECTLYRERYRRSLEAKVARAVE 75
>gnl|CDD|215645 PLN03246, PLN03246, 26S proteasome regulatory subunit; Provisional.
Length = 303
Score = 29.7 bits (67), Expect = 2.4
Identities = 22/91 (24%), Positives = 40/91 (43%), Gaps = 3/91 (3%)
Query: 107 DIKISALALLKMVMHAR---SGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQ 163
+ + L LL +V H V+G+LLG + V ++FA+P E + +
Sbjct: 7 KVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGSSFRGRVDVTNSFAVPFEEDDKDPSIW 66
Query: 164 AQAYEYMTAYIEAAKEVGRLENAIGWYHSHP 194
+ Y+ + K + E+ +GWY + P
Sbjct: 67 FLDHNYLESMFGMFKRINAKEHVVGWYSTGP 97
>gnl|CDD|148740 pfam07305, DUF1454, Protein of unknown function (DUF1454). This
family consists of several Enterobacterial sequences of
around 200 residues in length which are often known as
YiiQ proteins. The function of this family is unknown.
Length = 200
Score = 29.5 bits (66), Expect = 2.5
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 151 LPVEGTETRVNAQAQAYEYMTAYIEA 176
LP++G E + A+A+A EYM A I
Sbjct: 110 LPIQGPEQKA-AKAKALEYMAALIRH 134
>gnl|CDD|236460 PRK09300, PRK09300, tRNA splicing endonuclease; Reviewed.
Length = 330
Score = 29.6 bits (67), Expect = 2.5
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 7/39 (17%)
Query: 239 FRTYPKGYKPANEEP-------SEYQTIPLNKIEDFGVH 270
FR YP+G P + E SE +P + + +
Sbjct: 95 FRVYPRGSGPGDGESKYRVRVVSERDPLPFSDLIERKQL 133
>gnl|CDD|147544 pfam05410, Peptidase_C31, Porcine arterivirus-type cysteine
proteinase alpha. Corresponds to Merops family C31.
These peptidases are involved in viral polyprotein
processing in replication.
Length = 105
Score = 28.0 bits (62), Expect = 3.2
Identities = 16/54 (29%), Positives = 21/54 (38%), Gaps = 2/54 (3%)
Query: 194 PGYGCWLSGIDVSTQML--NQNFQEPFVAIVIDPVRTISAGKVCLGSFRTYPKG 245
P CWLS I +M N NFQ+ V + R L + Y +G
Sbjct: 16 PAGACWLSAIFPIARMTSGNHNFQQRLVRVAAVIYRDGQLTPKHLKELQVYERG 69
>gnl|CDD|182682 PRK10729, nudF, ADP-ribose pyrophosphatase NudF; Provisional.
Length = 202
Score = 28.9 bits (65), Expect = 3.4
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 122 ARSGGTLEVMGLLLGKIDANSMIVMDAFALPVEGTETRVNAQAQAYEYMTAYIEAAKEVG 181
A GGT E +++G++DA + + A E V ++ QAY+++ E G
Sbjct: 124 ASPGGTSERSSIMVGEVDATTASGIHGLADENEDIRVHVVSREQAYQWV--------EEG 175
Query: 182 RLENA 186
+++NA
Sbjct: 176 KIDNA 180
>gnl|CDD|131735 TIGR02688, TIGR02688, TIGR02688 family protein. Members of this
family are uncharacterized proteins sporadically
distributed in bacteria and archaea, about 470 amino
acids in length. Several members of this family appear
in public databases with annotation as ATP-dependent
protease La, despite the lack of similarity to families
TIGR00763 (ATP-dependent protease La) or pfam02190
(ATP-dependent protease La (LON) domain). This protein
is repeatedly found downstream of another
uncharacterized protein of about 880 amino acids in
length, described by model TIGR02687 [Hypothetical
proteins, Conserved].
Length = 449
Score = 29.3 bits (66), Expect = 4.5
Identities = 11/43 (25%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 312 ADYLTGQMCDLSDKLEQAESALVRNFLISESQERRPETKLMKA 354
+YL G+ C +L + VR+ L +++ R E +++K
Sbjct: 29 LEYLLGKYCATDGELIEEGIQKVRSIL-AKNYVRPNEAQIIKH 70
>gnl|CDD|151721 pfam11280, DUF3081, Protein of unknown function (DUF3081). This
family of proteins with unknown function appears to be
restricted to Gammaproteobacteria.
Length = 79
Score = 27.2 bits (61), Expect = 4.6
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 190 YHSHPGYGCWLSGIDVS 206
+ + GY CWL+ DV+
Sbjct: 33 WTDYDGYTCWLADNDVT 49
>gnl|CDD|185236 PRK15336, PRK15336, type III secretion system chaperone SpaK;
Provisional.
Length = 135
Score = 27.9 bits (62), Expect = 4.8
Identities = 12/19 (63%), Positives = 16/19 (84%)
Query: 134 LLGKIDANSMIVMDAFALP 152
L+G ID++S IV+D FALP
Sbjct: 23 LIGGIDSHSTIVLDLFALP 41
>gnl|CDD|227111 COG4770, COG4770, Acetyl/propionyl-CoA carboxylase, alpha subunit
[Lipid metabolism].
Length = 645
Score = 29.2 bits (66), Expect = 5.0
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 19/63 (30%)
Query: 139 DANSMIVM---DAFAL-PVEGTETRVNAQAQAYEYMTAYIEAAKEVGRLENAIGWYHSHP 194
DA+++ V +A + P A++Y + I+AA+ G AI HP
Sbjct: 36 DADALHVRMADEAVHIGPA--------PAAESYLDIDKIIDAARRTG--AQAI-----HP 80
Query: 195 GYG 197
GYG
Sbjct: 81 GYG 83
>gnl|CDD|227934 COG5647, COG5647, Cullin, a subunit of E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 773
Score = 28.6 bits (64), Expect = 6.7
Identities = 19/85 (22%), Positives = 36/85 (42%), Gaps = 10/85 (11%)
Query: 274 YYSLDVSYFKSSLDRRLLDSLWNKYWVNTLSSSSLLTNADYLTGQMCDLSDKLEQAESAL 333
Y ++SY+KS + L+ W Y + + LL+ +YL K+ + E L
Sbjct: 210 YKKENLSYYKSVFEPIFLEETWEFYEMESSEVIELLSVTEYLEKAH-----KILEREEEL 264
Query: 334 VRNFLISESQERRPETKLMKATKDC 358
V +L + + L++ +D
Sbjct: 265 VEIYLKVST-----KKPLLEVLEDV 284
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.132 0.393
Gapped
Lambda K H
0.267 0.0698 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,375,764
Number of extensions: 1819881
Number of successful extensions: 1415
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1395
Number of HSP's successfully gapped: 36
Length of query: 394
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 295
Effective length of database: 6,546,556
Effective search space: 1931234020
Effective search space used: 1931234020
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (27.0 bits)