RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4542
(273 letters)
>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 = 357 bits (919), Expect = e-125
Identities = 135/265 (50%), Positives = 185/265 (69%), Gaps = 4/265 (1%)
Query: 7 IKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEAELN 66
++VHPVVLF I+D++ERRN RVIGTLLGT +G VE+TNCF VPH E ++ V ++
Sbjct: 1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGTRSEGEVEITNCFAVPHNESEDQVAVDME 60
Query: 67 YAQDMFEMNQKVNPSELIVGWWATGDEVTSQSSVIHDYYIREC--KNPVHMTLDTNLKGP 124
Y + M+E++QKVNP E+IVGW+ATG E+T S++IHDYY REC NP+H+T+DT+L
Sbjct: 61 YHRTMYELHQKVNPKEVIVGWYATGSEITEHSALIHDYYSRECTSYNPIHLTVDTSLDDG 120
Query: 125 NMGIKGYVHVPIGVPGGKSGIMFTQIPAEVICYNSEVTGLRLLHKSI--KQGAVQPLSEL 182
M IK YV P+GVPG G MF IP E++ +E L LL K++ + S+L
Sbjct: 121 KMSIKAYVSSPLGVPGKTLGSMFVPIPLELLYSEAERVALDLLAKTLASPSRSAPLTSDL 180
Query: 183 TLVSEAADKLTVLIDHVLRYVDEVLANRITPDNSIGRQLLDMVNSVPSMTQEQFETMFNS 242
+ + +KL ++D VLRYV++VLA ++ DN+IGR L+D + SVP + E+FE MFNS
Sbjct: 181 EQLEASLEKLQEMLDRVLRYVEDVLAGKVKADNAIGRYLMDALTSVPKLDPEEFEKMFNS 240
Query: 243 NIKDLLMIMTLSQLTKTQLLLNEKL 267
+++DLLM+ LS LTKTQL L EKL
Sbjct: 241 SLQDLLMVTYLSNLTKTQLALAEKL 265
>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 = 113 bits (286), Expect = 4e-30
Identities = 79/274 (28%), Positives = 138/274 (50%), Gaps = 20/274 (7%)
Query: 9 VHPVVLFQIVDAFER-RNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEA---E 64
VHP+VL +VD + R S RV+G LLG+ KGV++VTN F VP +E ++ +
Sbjct: 5 VHPLVLLSVVDHYNRVAKGTSKRVVGVLLGSWKKGVLDVTNSFAVPFEEDEKDPSVWFLD 64
Query: 65 LNYAQDMFEMNQKVNPSELIVGWWATGDEVTSQSSVIHDYYIRECKNPVHMTLDTNLKGP 124
NY ++M+ M +KVN E IVGW++TG ++ I++ + R C NPV + +D K
Sbjct: 65 HNYLENMYGMFKKVNAKEKIVGWYSTGPKLRPNDLDINELFRRYCPNPVLVIIDVRPKDL 124
Query: 125 NMGIKGYVHV-PIGVPGGKSGIMFTQIPAEVICYNSEVTGLRLLHKSIKQGAVQPLSELT 183
+ + Y+ V + G + F +P+E+ +E G+ L + IK V T
Sbjct: 125 GLPTEAYIAVEEVHDDGTPTSKTFVHVPSEIGAEEAEEVGVEHLLRDIKDVTVS-----T 179
Query: 184 LVSEAADKLTVL------IDHVLRYVDEVLANRITPDNSIGRQLLDMVNSVPSMTQEQFE 237
L + +KL L + + Y+ V+ ++ ++ I L D+ N +P++ +
Sbjct: 180 LSTRVTNKLNSLKGLQSKLKEIKDYLQLVVEGKLPINHQIIYNLQDIFNLLPNLNLPELV 239
Query: 238 TMFNSNIKDLLMIMTLSQLTKTQL----LLNEKL 267
F D ++++ LS L ++ + L+N K+
Sbjct: 240 KAFAVKTNDQMLVIYLSSLIRSVIALHNLINNKI 273
>gnl|CDD|215645 PLN03246, PLN03246, 26S proteasome regulatory subunit; Provisional.
Length = 303
Score = 111 bits (279), Expect = 5e-29
Identities = 85/277 (30%), Positives = 142/277 (51%), Gaps = 23/277 (8%)
Query: 9 VHPVVLFQIVDAFERRNLDSH-RVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEA---E 64
VHP+VL IVD + R D+ RV+G LLG+ +G V+VTN F VP +E D+ +
Sbjct: 10 VHPLVLLSIVDHYNRVAKDTRKRVVGVLLGSSFRGRVDVTNSFAVPFEEDDKDPSIWFLD 69
Query: 65 LNYAQDMFEMNQKVNPSELIVGWWATGDEVTSQSSVIHDYYIRECKNPVHMTLDTNLKGP 124
NY + MF M +++N E +VGW++TG ++ IH+ + NPV + +D K
Sbjct: 70 HNYLESMFGMFKRINAKEHVVGWYSTGPKLRENDLDIHELFNDYVPNPVLVIIDVQPKEL 129
Query: 125 NMGIKGYVHVPIGV---PGGKSGIMFTQIPAEVICYNSEVTGLRLLHKSIKQGAVQPLSE 181
+ K Y + V KS +F +P+E+ + +E G+ L + +K V
Sbjct: 130 GIPTKAY-YAVEEVKENATQKSQKVFVHVPSEIGAHEAEEIGVEHLLRDVKDTTVS---- 184
Query: 182 LTLVSEAADKLTVL--IDHVLR----YVDEVLANRITPDNSIGRQLLDMVNSVPSMTQEQ 235
TL +E KLT L +D LR Y+D V+ ++ ++ I L D+ N +P++ E+
Sbjct: 185 -TLATEVTGKLTALKGLDARLREIRSYLDLVVEGKLPLNHEILYHLQDVFNLLPNLNVEE 243
Query: 236 FETMFNSNIKDLLMIMTLSQLTKTQL----LLNEKLT 268
F D+++++ LS L ++ + L+N K+
Sbjct: 244 LVKAFAVKTNDMMLVIYLSSLIRSVIALHNLINNKIL 280
>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 = 101 bits (254), Expect = 7e-27
Identities = 42/122 (34%), Positives = 70/122 (57%), Gaps = 5/122 (4%)
Query: 7 IKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEAELN 66
+++HP+VL I D + RR RVIG LLG VD +EVTN F +P E +E + +
Sbjct: 1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVDGDKIEVTNSFELPFDEEEESIFIDTE 60
Query: 67 YAQDMFEMNQKVNPSELIVGWWATG----DEVTSQSSVIHDYYIRE-CKNPVHMTLDTNL 121
Y + + +++KV P E IVGW++ G +E++ + +H + +NP+ + LD +L
Sbjct: 61 YLEKRYNLHKKVYPQEKIVGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSL 120
Query: 122 KG 123
+
Sbjct: 121 QS 122
>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 = 81.3 bits (201), Expect = 1e-19
Identities = 40/115 (34%), Positives = 57/115 (49%), Gaps = 8/115 (6%)
Query: 5 VSIKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVDK-GVVEVTNCFCVPHKE---YDEM 60
++ +HP+VL +IVD R V+G LLGT++ V+EVTN F +P E E
Sbjct: 3 RTVVIHPLVLLKIVDHARRGGKSGEEVMGVLLGTLEGDRVIEVTNSFALPQSETEDDVEA 62
Query: 61 VEAELNYAQDMFEMNQKVNPSELIVGWWATG---DEVTSQSSV-IHDYYIRECKN 111
VE + Y + M EM +KVN E +VGW+ + S V + Y R
Sbjct: 63 VELDHEYMEKMLEMLKKVNRDEEVVGWYHSHPGYGCWLSSVDVHTQELYQRMIPE 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 = 80.5 bits (199), Expect = 6e-19
Identities = 35/118 (29%), Positives = 53/118 (44%), Gaps = 7/118 (5%)
Query: 7 IKVHPVVLFQIVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVP-HKEYDEMVEAEL 65
+KVHP+V I+ R + V G LLG +K EV F VP + D + E +
Sbjct: 2 VKVHPLVPLNILKHAIRDGPE--EVCGVLLGKSNKDRPEVKEVFAVPNEPQDDSVQEYDE 59
Query: 66 NYAQDMFEMNQKVNPSELIVGWWATGDEVTSQSS----VIHDYYIRECKNPVHMTLDT 119
+Y+ M E +KVN IVGW+ + + + S H+ Y V + +D
Sbjct: 60 DYSHLMDEELKKVNKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDP 117
>gnl|CDD|205193 pfam13012, MitMem_reg, Maintenance of mitochondrial structure and
function. This is C-terminal to the Mov24 region of the
yeast proteasomal subunit Rpn11 and seems likely to
regulate the mitochondrial fission and tubulation
processes, ie the outer mitochondrial membrane proteins.
This function appears to be unrelated to the proteasome
activity of the N-terminal region.
Length = 115
Score = 75.3 bits (186), Expect = 2e-17
Identities = 28/111 (25%), Positives = 58/111 (52%), Gaps = 1/111 (0%)
Query: 159 SEVTGLRLLHKSIKQGAVQPLSE-LTLVSEAADKLTVLIDHVLRYVDEVLANRITPDNSI 217
+E G+ L + + + LS L L +A L + + Y+++V+ ++ P++ I
Sbjct: 3 AEQIGVEHLLRGLNRHYYSTLSRKLELEQKALKNLHKRLWTIGLYLEDVIDGKLPPNHEI 62
Query: 218 GRQLLDMVNSVPSMTQEQFETMFNSNIKDLLMIMTLSQLTKTQLLLNEKLT 268
R+L ++N +P+ ++FE FN D L+++ L +L + Q L+E +
Sbjct: 63 LRKLQSLLNLLPNYDNKEFEEEFNVETNDQLLVVYLGKLDRKQHALHELIN 113
>gnl|CDD|163694 cd08063, MPN_CSN6, Mpr1p, Pad1p N-terminal (MPN) domains without
catalytic isopeptidase activity, found in COP9
signalosome complex subunit 6. CSN6 (COP9 signalosome
subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one
of the eight subunits of COP9 signalosome, 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. CSN6 is an MPN-domain protein that directly
interacts with the MPN+-domain subunit CSN5. It is
cleaved during apoptosis by activated caspases. CSN6
processing occurs in CSN/CRL (cullin-RING Ub ligase)
complexes and is followed by the cleavage of Rbx1, the
direct interaction partner of CSN6. CSN6 cleavage
enhances CSN-mediated deneddylating activity (i.e.
cleavage of ubiquitin-like protein Nedd8 (neural
precursor cell expressed, developmentally downregulated
8)) in the cullin 1 in cells. The cleavage of Rbx1 and
increased deneddylation of cullins inactivate CRLs and
presumably stabilize pro-apoptotic factors for final
apoptotic steps. While CSN6 shows a typical MPN
metalloprotease fold, it lacks the canonical JAMM motif,
and therefore does not show catalytic isopeptidase
activity.
Length = 288
Score = 65.4 bits (160), Expect = 2e-12
Identities = 64/276 (23%), Positives = 120/276 (43%), Gaps = 20/276 (7%)
Query: 5 VSIKVHPVVLFQIVDAFER----RNLDSHRVIGTLLGTVDKGVVEVTNCF-CVPHKEYDE 59
+S+K+HP+V+ I D R + RV+G LLG D +E+ N F D
Sbjct: 1 LSVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDGREIEIENSFELKYDTNEDG 60
Query: 60 MVEAELNYAQDMFEMNQKVNPSELIVGWWATGDEVTSQSSV-IHDYYIRECKNPVHMTLD 118
+ + + + E ++V VGW+ TG ++S + IH + ++PV + LD
Sbjct: 61 EIVLDKEFLETRLEQFKQVFKDLDFVGWYTTGPGGPTESDLPIHKQILEINESPVLLLLD 120
Query: 119 --TNLKGPNMGIKGYVHVPIGVPGGKSGIMFTQIP-------AEVICYNSEVTGLRLLHK 169
N G ++ + Y V + + G++ + F ++P AE I + G
Sbjct: 121 PEANASGKDLPVTIYESV-LELVDGEATLRFRELPYTIETGEAERIGVDHVARGGASGSS 179
Query: 170 SIKQGAVQPLSELTLVSEAADKLTVLIDHVLRYVDEVLANRITPDNSIGRQLLDMVNSVP 229
A ++ + ++ ++++ Y+ V + PD+SI R + + + +P
Sbjct: 180 EKSTVAAHLQAQHNAIKMLNSRVELILE----YLKAVPVGEVPPDHSILRSISALCSRLP 235
Query: 230 SMTQEQFETMFNSNIKDLLMIMTLSQLTKTQLLLNE 265
+ E F + D+L++ L+ LTK LNE
Sbjct: 236 VLKSEAFREELLAEYNDVLLVAYLATLTKGCNTLNE 271
>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 = 45.3 bits (108), Expect = 1e-05
Identities = 23/60 (38%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 31 VIGTLLGTVDKGVVEVTNCFCVPHKEYDE---MVEAELNYAQDMFEMNQKVNPSELIVGW 87
V G LLG G +EVTNCF P E D+ E +Y +M + ++VN VGW
Sbjct: 25 VQGQLLGLDVGGTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVDHNHVGW 84
>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 = 37.5 bits (87), Expect = 0.001
Identities = 29/107 (27%), Positives = 45/107 (42%), Gaps = 10/107 (9%)
Query: 17 IVDAFERRNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEAELNYAQDMFEMNQ 76
+DA + N VIG L G+ K V++V VP E D + N M+ +
Sbjct: 4 FLDAAKSINGK--EVIGLLYGSKTKKVLDVDEVIAVPFDEGD----KDDNVWFLMYLDFK 57
Query: 77 KVNPSELIVGWWATGDEVTSQSS----VIHDYYIRECKNPVHMTLDT 119
K+N IVGW+ T + + S H+ + R V + +D
Sbjct: 58 KLNAGLRIVGWYHTHPKPSCFLSPNDLATHELFQRYFPEKVMIIVDV 104
>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 = 35.3 bits (82), Expect = 0.021
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 31 VIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEAELNYAQDM--FEMNQKVNPSELIVGW 87
V+G +LG VD + V + F +P + + V A+ + + M +EM ++ E +VGW
Sbjct: 34 VMGLMLGKVDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLKQTGRPENVVGW 92
>gnl|CDD|216101 pfam00755, Carn_acyltransf, Choline/Carnitine o-acyltransferase.
Length = 590
Score = 30.3 bits (69), Expect = 1.1
Identities = 10/48 (20%), Positives = 20/48 (41%), Gaps = 9/48 (18%)
Query: 195 LIDHVLRYVDEVLANRITPDNSIGRQLLDMVNSVPSMTQEQFETMFNS 242
LI +L + + + P+ ++G L M Q+ +FN+
Sbjct: 108 LIHGILLFKRLLDREELKPETALGNTPLCM---------NQYYRLFNT 146
>gnl|CDD|235146 PRK03640, PRK03640, O-succinylbenzoic acid--CoA ligase;
Provisional.
Length = 483
Score = 28.8 bits (65), Expect = 3.6
Identities = 9/28 (32%), Positives = 17/28 (60%)
Query: 241 NSNIKDLLMIMTLSQLTKTQLLLNEKLT 268
+ ++ +L+I L QL +LLN +L+
Sbjct: 60 KNGMEMILVIHALQQLGAVAVLLNTRLS 87
>gnl|CDD|187587 cd05326, secoisolariciresinol-DH_like_SDR_c, secoisolariciresinol
dehydrogenase (secoisolariciresinol-DH)-like, classical
(c) SDRs. Podophyllum secoisolariciresinol-DH is a homo
tetrameric, classical SDR that catalyzes the
NAD-dependent conversion of (-)-secoisolariciresinol to
(-)-matairesinol via a (-)-lactol intermediate.
(-)-Matairesinol is an intermediate to various
8'-lignans, including the cancer-preventive mammalian
lignan, and those involved in vascular plant defense.
This subgroup also includes rice momilactone A synthase
which catalyzes the conversion of
3beta-hydroxy-9betaH-pimara-7,15-dien-19,6beta-olide
into momilactone A, Arabidopsis ABA2 which during
abscisic acid (ABA) biosynthesis, catalyzes the
conversion of xanthoxin to abscisic aldehyde and, maize
Tasselseed2 which participate in the maize sex
determination pathway. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering). In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering)
contributing to the active site; while substrate binding
is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 249
Score = 27.8 bits (62), Expect = 5.4
Identities = 14/46 (30%), Positives = 17/46 (36%), Gaps = 3/46 (6%)
Query: 104 YYIRECKNP-VHMTLDTNLKGPNMGIKGYVHVPIGVPGGKSGIMFT 148
Y I E LD N+ G +G K V I P K I+
Sbjct: 95 YSILETSLEEFERVLDVNVYGAFLGTKHAARVMI--PAKKGSIVSV 138
>gnl|CDD|176520 cd08578, GDPD_NUC-2_fungi, Putative glycerophosphodiester
phosphodiesterase domain of ankyrin repeat protein NUC-2
and similar proteins. This subfamily corresponds to a
putative glycerophosphodiester phosphodiesterase domain
(GDPD) present in Neurospora crassa ankyrin repeat
protein NUC-2 and its Saccharomyces cerevisiae
counterpart, Phosphate system positive regulatory
protein PHO81. Some uncharecaterized NUC-2 sequence
homologs are also included in this family. NUC-2 plays
an important role in the phosphate-regulated signal
transduction pathway in Neurospora crassa. It shows high
similarity to a cyclin-dependent kinase inhibitory
protein PHO81, which is part of the phosphate regulatory
cascade in S. cerevisiae. Both NUC-2 and PHO81 have
multi-domain architecture, including an SPX N-terminal
domain following by several ankyrin repeats and a
putative C-terminal GDPD domain with unknown function.
Although the putative GDPD domain displays sequence
homology to that of bacterial glycerophosphodiester
phosphodiesterases (GP-GDEs, EC 3.1.4.46), the residues
essential for interactions with the substrates and
calcium ions in bacterial GP-GDEs are not conserved in
members of this family, which suggests the function of
putative GDPD domains in these proteins might be
distinct from those in typical bacterial GP-GDEs.
Length = 300
Score = 27.7 bits (62), Expect = 7.6
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 228 VPSMTQEQFETMFNSNIKDLL-MIMTLSQLTKTQLLLNEKLTLLTSL 273
V +T EQ E++ + ++ DL I + L + LL+ ++ L +L
Sbjct: 61 VSDLTAEQLESILDYSLDDLNSEISDMVDLKR---LLSSRVVSLETL 104
>gnl|CDD|206046 pfam13875, DUF4202, Domain of unknown function (DUF4202). This
family of proteins is found in bacteria, archaea and
eukaryotes. Proteins in this family are typically
between 187 and 205 amino acids in length. There are
two conserved sequence motifs: LED and KMS. The
function of these proteins is unknown, although many
are incorrectly annotated as glutamyl tRNA synthetases.
Length = 185
Score = 27.2 bits (61), Expect = 8.0
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 53 PHKEYDEMVE--AELNYAQDMFEMNQKVNP--SELI 84
P++E + E EL YAQ M E ++ P SE +
Sbjct: 16 PNRETVDGKEVPKELLYAQRMTEWLARLAPDASEAL 51
>gnl|CDD|236831 PRK11052, malQ, 4-alpha-glucanotransferase; Provisional.
Length = 695
Score = 27.5 bits (62), Expect = 8.0
Identities = 11/24 (45%), Positives = 13/24 (54%), Gaps = 4/24 (16%)
Query: 26 LDSHR----VIGTLLGTVDKGVVE 45
L+S R VIG LGTV +V
Sbjct: 486 LESQRHRCMVIGEDLGTVPVEIVG 509
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 0.135 0.387
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: 13,497,552
Number of extensions: 1271226
Number of successful extensions: 1070
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1052
Number of HSP's successfully gapped: 28
Length of query: 273
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 178
Effective length of database: 6,723,972
Effective search space: 1196867016
Effective search space used: 1196867016
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 (21.7 bits)
S2: 58 (26.2 bits)