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Asym. Unit
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Asym.Unit (108 KB)
Biol.Unit 1 (103 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE S18Y VARIANT OF UBIQUITIN CARBOXY TERMINAL HYDROLASE L1 BOUND TO UBIQUITIN VINYLMETHYLESTER.
Authors
:
C. Das, D. Boudreaux, T. Maiti
Date
:
26 Jul 09 (Deposition) - 16 Jun 10 (Release) - 16 Jun 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Enzyme-Suicide Substrate Complex, Cytoplasm, Disease Mutation, Glycoprotein, Hydrolase, Ligase, Oxidation, Polymorphism, Protease, Thiol Protease, Ubl Conjugation Pathway, Isopeptide Bond, Nucleus, Phosphoprotein, Ubl Conjugation, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. A. Boudreaux, T. K. Maiti, C. W. Davies, C. Das
Ubiquitin Vinyl Methyl Ester Binding Orients The Misaligned Active Site Of The Ubiquitin Hydrolase Uchl1 Into Productive Conformation.
Proc. Natl. Acad. Sci. Usa V. 107 9117 2010
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: METHYL 4-AMINOBUTANOATE (GVEa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GVE
1
Ligand/Ion
METHYL 4-AMINOBUTANOATE
[
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]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU A:55 , GLN A:84 , ASN A:88 , CYS A:90 , PHE A:160 , GLY B:75
BINDING SITE FOR RESIDUE GVE B 76
[
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SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_070875 (E7A, chain A, )
2: VAR_015677 (Y18Y, chain A, )
3: VAR_015678 (I93M, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_070875
E
7
A
UCHL1_HUMAN
Disease (NDGOA)
---
A
E
7
A
2
UniProt
VAR_015677
S
18
Y
UCHL1_HUMAN
Polymorphism
5030732
A
Y
18
Y
3
UniProt
VAR_015678
I
93
M
UCHL1_HUMAN
Disease (PARK5)
---
A
I
93
M
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_2 (B:1-75,B:1-75,-|-|B:1-75,-|-|-|-|-...)
2: UBIQUITIN_1 (B:27-52,B:27-52,-|-|B:27-52,-|-|-|...)
3: UCH_1 (A:84-100)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UBIQUITIN_2
PS50053
Ubiquitin domain profile.
RS27A_HUMAN
1-76
1
B:1-75
RL40_HUMAN
1-76
1
B:1-75
UBB_HUMAN
1-76
77-152
153-228
1
-
-
B:1-75
UBC_HUMAN
1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
1
-
-
-
-
-
-
-
-
B:1-75
2
UBIQUITIN_1
PS00299
Ubiquitin domain signature.
RS27A_HUMAN
27-52
1
B:27-52
RL40_HUMAN
27-52
1
B:27-52
UBB_HUMAN
27-52
103-128
179-204
1
-
-
B:27-52
UBC_HUMAN
27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
1
-
-
-
-
-
-
-
-
B:27-52
3
UCH_1
PS00140
Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site.
UCHL1_HUMAN
84-100
1
A:84-100
[
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Exons
(10, 10)
Info
All Exons
Exon 1.4a (A:1-11)
Exon 1.5a (A:12-15)
Exon 1.5d (A:16-58)
Exon 1.6b (A:59-109)
Exon 1.7a (A:109-137)
Exon 1.8 (A:138-153)
Exon 1.9a (A:154-176)
Exon 1.10a (A:176-195)
Exon 1.11h (A:196-223)
Exon 2.2 (B:1-75)
View:
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All Exon Boundaries
01: Boundary -/1.4a
02: Boundary 1.4a/1.5a
03: Boundary 1.5a/1.5d
04: Boundary 1.5d/1.6b
05: Boundary 1.6b/1.7a
06: Boundary 1.7a/1.8
07: Boundary 1.8/1.9a
08: Boundary 1.9a/1.10a
09: Boundary 1.10a/1.11h
10: Boundary 1.11h/-
11: Boundary 2.1/2.2
12: Boundary 2.2/-
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.4a
ENST00000284440
4a
ENSE00001014976
chr4:
41258850-41259026
177
UCHL1_HUMAN
1-11
11
1
A:1-11
11
1.5a
ENST00000284440
5a
ENSE00001700600
chr4:
41259132-41259143
12
UCHL1_HUMAN
12-15
4
1
A:12-15
4
1.5d
ENST00000284440
5d
ENSE00002143077
chr4:
41259626-41259754
129
UCHL1_HUMAN
16-58
43
1
A:16-58
43
1.6b
ENST00000284440
6b
ENSE00001720890
chr4:
41262664-41262814
151
UCHL1_HUMAN
59-109
51
1
A:59-109
51
1.7a
ENST00000284440
7a
ENSE00001014975
chr4:
41263732-41263817
86
UCHL1_HUMAN
109-137
29
1
A:109-137
29
1.8
ENST00000284440
8
ENSE00001014973
chr4:
41263893-41263940
48
UCHL1_HUMAN
138-153
16
1
A:138-153
16
1.9a
ENST00000284440
9a
ENSE00001014969
chr4:
41265242-41265308
67
UCHL1_HUMAN
154-176
23
1
A:154-176
23
1.10a
ENST00000284440
10a
ENSE00001014974
chr4:
41266120-41266178
59
UCHL1_HUMAN
176-195
20
1
A:176-195
20
1.11h
ENST00000284440
11h
ENSE00001852993
chr4:
41270004-41270446
443
UCHL1_HUMAN
196-223
28
1
A:196-223
28
2.1
ENST00000339647
1
ENSE00001257182
chr12:
125399577-125399133
445
UBC_HUMAN
-
0
0
-
-
2.2
ENST00000339647
2
ENSE00001406973
chr12:
125398320-125396194
2127
UBC_HUMAN
1-686
686
1
B:1-75
75
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3ifwb_ (B:)
2a: SCOP_d3ifwa_ (A:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
beta-Grasp (ubiquitin-like)
(1032)
Superfamily
:
Ubiquitin-like
(546)
Family
:
Ubiquitin-related
(337)
Protein domain
:
Ubiquitin
(162)
Human (Homo sapiens) [TaxId: 9606]
(121)
1a
d3ifwb_
B:
Fold
:
Cysteine proteinases
(392)
Superfamily
:
Cysteine proteinases
(392)
Family
:
Ubiquitin carboxyl-terminal hydrolase UCH-L
(10)
Protein domain
:
automated matches
(4)
Human (Homo sapiens) [TaxId: 9606]
(4)
2a
d3ifwa_
A:
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_3ifwA00 (A:1-223)
2a: CATH_3ifwB00 (B:1-75)
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Topologies
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Ubiquitin C-terminal Hydrolase UCH-l3
(8)
Homologous Superfamily
:
Ubiquitin C-terminal Hydrolase Uch-l3
(8)
Human (Homo sapiens)
(7)
1a
3ifwA00
A:1-223
Architecture
:
Roll
(3276)
Topology
:
Ubiquitin-like (UB roll)
(674)
Homologous Superfamily
:
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
(286)
Human (Homo sapiens)
(177)
2a
3ifwB00
B:1-75
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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