RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12650
(90 letters)
>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 = 78.0 bits (193), Expect = 7e-20
Identities = 32/59 (54%), Positives = 41/59 (69%), Gaps = 8/59 (13%)
Query: 1 VQSELHITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIHWQLHITHLLIPKQ 59
+ ITHL+IPKQ+GT+DSC T +EEE+F QD+++LITLGWIH TH P Q
Sbjct: 37 SNNAFFITHLIIPKQSGTSDSCQTTNEEELFDFQDQHDLITLGWIH-----TH---PTQ 87
Score = 76.5 bits (189), Expect = 3e-19
Identities = 28/43 (65%), Positives = 36/43 (83%)
Query: 48 QLHITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIH 90
ITHL+IPKQ+GT+DSC T +EEE+F QD+++LITLGWIH
Sbjct: 40 AFFITHLIIPKQSGTSDSCQTTNEEELFDFQDQHDLITLGWIH 82
>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 = 32.2 bits (73), Expect = 0.010
Identities = 17/52 (32%), Positives = 26/52 (50%)
Query: 1 VQSELHITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIHWQLHIT 52
+E H+++PKQ+ DSC + EE+F Q L+ +GW H T
Sbjct: 27 THNEFTDKHVIVPKQSAGPDSCTGENVEELFNVQTGRPLLVVGWYHSHPTFT 78
Score = 30.6 bits (69), Expect = 0.046
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 46 HWQLHITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIH 90
H + H+++PKQ+ DSC + EE+F Q L+ +GW H
Sbjct: 28 HNEFTDKHVIVPKQSAGPDSCTGENVEELFNVQTGRPLLVVGWYH 72
>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 = 31.7 bits (72), Expect = 0.019
Identities = 9/71 (12%), Positives = 20/71 (28%)
Query: 4 ELHITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIHWQLHITHLLIPKQAGTA 63
L + ++ + + L +GW H + L P T
Sbjct: 28 VLDVDEVIAVPFDEGDKDDNVWFLMYLDFKKLNAGLRIVGWYHTHPKPSCFLSPNDLATH 87
Query: 64 DSCITHHEEEI 74
+ + E++
Sbjct: 88 ELFQRYFPEKV 98
Score = 27.5 bits (61), Expect = 0.68
Identities = 5/47 (10%), Positives = 11/47 (23%)
Query: 44 WIHWQLHITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIH 90
L + ++ + + L +GW H
Sbjct: 24 KTKKVLDVDEVIAVPFDEGDKDDNVWFLMYLDFKKLNAGLRIVGWYH 70
>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 = 28.1 bits (63), Expect = 0.40
Identities = 8/58 (13%), Positives = 17/58 (29%), Gaps = 7/58 (12%)
Query: 5 LHITHLLIPKQAGTADSCITHHEEEIFAC-------QDKYNLITLGWIHWQLHITHLL 55
+ +T+ Q+ T D + + + + +GW H L
Sbjct: 43 IEVTNSFALPQSETEDDVEAVELDHEYMEKMLEMLKKVNRDEEVVGWYHSHPGYGCWL 100
Score = 27.4 bits (61), Expect = 0.73
Identities = 7/49 (14%), Positives = 16/49 (32%), Gaps = 7/49 (14%)
Query: 49 LHITHLLIPKQAGTADSCITHHEEEIFAC-------QDKYNLITLGWIH 90
+ +T+ Q+ T D + + + + +GW H
Sbjct: 43 IEVTNSFALPQSETEDDVEAVELDHEYMEKMLEMLKKVNRDEEVVGWYH 91
>gnl|CDD|218716 pfam05721, PhyH, Phytanoyl-CoA dioxygenase (PhyH). This family is
made up of several eukaryotic phytanoyl-CoA dioxygenase
(PhyH) proteins, ectoine hydroxylases and a number of
bacterial deoxygenases. PhyH is a peroxisomal enzyme
catalyzing the first step of phytanic acid
alpha-oxidation. PhyH deficiency causes Refsum's disease
(RD) which is an inherited neurological syndrome
biochemically characterized by the accumulation of
phytanic acid in plasma and tissues.
Length = 213
Score = 25.5 bits (56), Expect = 3.8
Identities = 12/47 (25%), Positives = 16/47 (34%)
Query: 44 WIHWQLHITHLLIPKQAGTADSCITHHEEEIFACQDKYNLITLGWIH 90
+ Q L I KQ GT H++ F L+ WI
Sbjct: 86 ALGLQSMYQDLSIFKQPGTGGEVSPWHQDYTFLPTRPAELVVNVWIA 132
>gnl|CDD|236924 PRK11539, PRK11539, ComEC family competence protein; Provisional.
Length = 755
Score = 25.0 bits (55), Expect = 6.2
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 42 LGWIHWQLHITHLLIPKQAG 61
L +H QL IT LL+P Q
Sbjct: 363 LRLLHLQLGITLLLMPLQIL 382
>gnl|CDD|219825 pfam08405, Calici_PP_N, Viral polyprotein N-terminal. This domain
is found at the N-terminus of non-structural viral
polyproteins of the Caliciviridae subfamily.
Length = 358
Score = 24.4 bits (53), Expect = 9.7
Identities = 13/29 (44%), Positives = 15/29 (51%)
Query: 1 VQSELHITHLLIPKQAGTADSCITHHEEE 29
V S H+T LL KQ+ A I EEE
Sbjct: 298 VISNNHLTQLLRDKQSAAAYMRILDLEEE 326
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
0.324 0.137 0.460
Gapped
Lambda K H
0.267 0.0641 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,436,348
Number of extensions: 331359
Number of successful extensions: 217
Number of sequences better than 10.0: 1
Number of HSP's gapped: 217
Number of HSP's successfully gapped: 15
Length of query: 90
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 32
Effective length of database: 8,365,070
Effective search space: 267682240
Effective search space used: 267682240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.4 bits)