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1J04
Biol. Unit 1
Info
Asym.Unit (69 KB)
Biol.Unit 1 (65 KB)
Biol.Unit 2 (127 KB)
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(1)
Title
:
STRUCTURAL MECHANISM OF ENZYME MISTARGETING IN HEREDITARY KIDNEY STONE DISEASE IN VITRO
Authors
:
X. Zhang, S. Djordjevic, M. Bartlam, S. Ye, Z. Rao, C. J. Danpure
Date
:
30 Oct 02 (Deposition) - 11 Nov 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Biol. Unit 2: A (2x)
Keywords
:
Transferase, Aminotransferase, Pyridoxal Phosphate
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Djordjevic, X. Zhang, M. Bartlam, S. Ye, Z. Rao, C. J. Danpure
Structural Implications Of A G170R Mutation Of Alanine:Glyoxylate Aminotransferase That Is Associated With Peroxisome-To-Mitochondrion Mistargeting.
Acta Crystallogr. , Sect. F V. 66 233 2010
[
close entry info
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Hetero Components
(3, 9)
Info
All Hetero Components
1a: (AMINOOXY)ACETIC ACID (AOAa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
3a: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AOA
1
Ligand/Ion
(AMINOOXY)ACETIC ACID
2
GOL
7
Ligand/Ion
GLYCEROL
3
LLP
1
Mod. Amino Acid
2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PRO A:28 , GLY A:29 , LLP A:209 , MET A:348 , ARG A:360
BINDING SITE FOR RESIDUE AOA A 1001
2
AC2
SOFTWARE
LEU A:24 , ARG A:71 , ASP A:196 , PHE A:343
BINDING SITE FOR RESIDUE GOL A 1002
3
AC3
SOFTWARE
LYS A:228 , GLN A:290 , ARG A:370 , GLU A:371
BINDING SITE FOR RESIDUE GOL A 1003
4
AC4
SOFTWARE
SER A:19 , ASP A:52 , GLN A:55 , GLU A:59
BINDING SITE FOR RESIDUE GOL A 1004
5
AC5
SOFTWARE
GLN A:110 , ARG A:111 , TRP A:246
BINDING SITE FOR RESIDUE GOL A 1006
6
AC6
SOFTWARE
LEU A:278
BINDING SITE FOR RESIDUE GOL A 1007
7
AC7
SOFTWARE
LEU A:7 , ASN A:22 , ARG A:170 , ASP A:196
BINDING SITE FOR RESIDUE GOL A 1008
8
AC8
SOFTWARE
GLN A:137 , GLU A:138 , GLU A:141
BINDING SITE FOR RESIDUE GOL A 1009
[
close Site info
]
SAPs(SNPs)/Variants
(41, 41)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_060547 (T9N, chain A, )
02: VAR_000587 (P11L, chain A, )
03: VAR_048236 (N22S, chain A, )
04: VAR_000588 (G41R, chain A, )
05: VAR_010969 (G41V, chain A, )
06: VAR_008878 (G82E, chain A, )
07: VAR_060548 (G82R, chain A, )
08: VAR_060549 (W108R, chain A, )
09: VAR_060550 (A112D, chain A, )
10: VAR_010971 (G116R, chain A, )
11: VAR_000589 (F152I, chain A, )
12: VAR_060552 (L153V, chain A, )
13: VAR_010972 (G156R, chain A, )
14: VAR_060553 (S158L, chain A, )
15: VAR_060554 (G161R, chain A, )
16: VAR_000590 (R170R, chain A, )
17: VAR_060555 (C173Y, chain A, )
18: VAR_010973 (D183N, chain A, )
19: VAR_000591 (S187F, chain A, )
20: VAR_060556 (G190R, chain A, )
21: VAR_060557 (M195R, chain A, )
22: VAR_060558 (D201E, chain A, )
23: VAR_000592 (S205P, chain A, )
24: VAR_060559 (S218L, chain A, )
25: VAR_008879 (R233C, chain A, )
26: VAR_008880 (R233H, chain A, )
27: VAR_060560 (R233L, chain A, )
28: VAR_060561 (D243H, chain A, )
29: VAR_008881 (I244T, chain A, )
30: VAR_060562 (C253R, chain A, )
31: VAR_060563 (I279M, chain A, )
32: VAR_060564 (I279T, chain A, )
33: VAR_060565 (A280V, chain A, )
34: VAR_060566 (S287T, chain A, )
35: VAR_060567 (R289C, chain A, )
36: VAR_048237 (A295T, chain A, )
37: VAR_060569 (L298P, chain A, )
38: VAR_060570 (V326I, chain A, )
39: VAR_060571 (V336D, chain A, )
40: VAR_000593 (I340M, chain A, )
41: VAR_060572 (G350D, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_060547
T
9
N
SPYA_HUMAN
Disease (HP1)
---
A
T
9
N
02
UniProt
VAR_000587
P
11
L
SPYA_HUMAN
Polymorphism
34116584
A
P
11
L
03
UniProt
VAR_048236
N
22
S
SPYA_HUMAN
Polymorphism
34885252
A
N
22
S
04
UniProt
VAR_000588
G
41
R
SPYA_HUMAN
Disease (HP1)
---
A
G
41
R
05
UniProt
VAR_010969
G
41
V
SPYA_HUMAN
Disease (HP1)
---
A
G
41
V
06
UniProt
VAR_008878
G
82
E
SPYA_HUMAN
Disease (HP1)
---
A
G
82
E
07
UniProt
VAR_060548
G
82
R
SPYA_HUMAN
Disease (HP1)
---
A
G
82
R
08
UniProt
VAR_060549
W
108
R
SPYA_HUMAN
Disease (HP1)
---
A
W
108
R
09
UniProt
VAR_060550
A
112
D
SPYA_HUMAN
Disease (HP1)
---
A
A
112
D
10
UniProt
VAR_010971
G
116
R
SPYA_HUMAN
Disease (HP1)
---
A
G
116
R
11
UniProt
VAR_000589
F
152
I
SPYA_HUMAN
Disease (HP1)
---
A
F
152
I
12
UniProt
VAR_060552
L
153
V
SPYA_HUMAN
Disease (HP1)
---
A
L
153
V
13
UniProt
VAR_010972
G
156
R
SPYA_HUMAN
Disease (HP1)
---
A
G
156
R
14
UniProt
VAR_060553
S
158
L
SPYA_HUMAN
Disease (HP1)
---
A
S
158
L
15
UniProt
VAR_060554
G
161
R
SPYA_HUMAN
Disease (HP1)
---
A
G
161
R
16
UniProt
VAR_000590
G
170
R
SPYA_HUMAN
Disease (HP1)
---
A
R
170
R
17
UniProt
VAR_060555
C
173
Y
SPYA_HUMAN
Disease (HP1)
---
A
C
173
Y
18
UniProt
VAR_010973
D
183
N
SPYA_HUMAN
Disease (HP1)
---
A
D
183
N
19
UniProt
VAR_000591
S
187
F
SPYA_HUMAN
Disease (HP1)
---
A
S
187
F
20
UniProt
VAR_060556
G
190
R
SPYA_HUMAN
Disease (HP1)
---
A
G
190
R
21
UniProt
VAR_060557
M
195
R
SPYA_HUMAN
Disease (HP1)
---
A
M
195
R
22
UniProt
VAR_060558
D
201
E
SPYA_HUMAN
Disease (HP1)
---
A
D
201
E
23
UniProt
VAR_000592
S
205
P
SPYA_HUMAN
Disease (HP1)
---
A
S
205
P
24
UniProt
VAR_060559
S
218
L
SPYA_HUMAN
Disease (HP1)
---
A
S
218
L
25
UniProt
VAR_008879
R
233
C
SPYA_HUMAN
Disease (HP1)
---
A
R
233
C
26
UniProt
VAR_008880
R
233
H
SPYA_HUMAN
Disease (HP1)
---
A
R
233
H
27
UniProt
VAR_060560
R
233
L
SPYA_HUMAN
Disease (HP1)
---
A
R
233
L
28
UniProt
VAR_060561
D
243
H
SPYA_HUMAN
Disease (HP1)
---
A
D
243
H
29
UniProt
VAR_008881
I
244
T
SPYA_HUMAN
Disease (HP1)
---
A
I
244
T
30
UniProt
VAR_060562
C
253
R
SPYA_HUMAN
Disease (HP1)
---
A
C
253
R
31
UniProt
VAR_060563
I
279
M
SPYA_HUMAN
Disease (HP1)
---
A
I
279
M
32
UniProt
VAR_060564
I
279
T
SPYA_HUMAN
Polymorphism
140992177
A
I
279
T
33
UniProt
VAR_060565
A
280
V
SPYA_HUMAN
Polymorphism
73106685
A
A
280
V
34
UniProt
VAR_060566
S
287
T
SPYA_HUMAN
Disease (HP1)
---
A
S
287
T
35
UniProt
VAR_060567
R
289
C
SPYA_HUMAN
Disease (HP1)
---
A
R
289
C
36
UniProt
VAR_048237
A
295
T
SPYA_HUMAN
Polymorphism
13408961
A
A
295
T
37
UniProt
VAR_060569
L
298
P
SPYA_HUMAN
Disease (HP1)
---
A
L
298
P
38
UniProt
VAR_060570
V
326
I
SPYA_HUMAN
Polymorphism
115057148
A
V
326
I
39
UniProt
VAR_060571
V
336
D
SPYA_HUMAN
Disease (HP1)
---
A
V
336
D
40
UniProt
VAR_000593
I
340
M
SPYA_HUMAN
Polymorphism
4426527
A
I
340
M
41
UniProt
VAR_060572
G
350
D
SPYA_HUMAN
Disease (HP1)
---
A
G
350
D
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: AA_TRANSFER_CLASS_5 (A:200-220)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AA_TRANSFER_CLASS_5
PS00595
Aminotransferases class-V pyridoxal-phosphate attachment site.
SPYA_HUMAN
200-220
1
A:200-220
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1j04a_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PLP-dependent transferase-like
(627)
Superfamily
:
PLP-dependent transferases
(625)
Family
:
Cystathionine synthase-like
(64)
Protein domain
:
Alanine-glyoxylate aminotransferase
(4)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1j04a_
A:
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1j04A02 (A:34-282)
2a: CATH_1j04A01 (A:4-33,A:283-390)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aspartate Aminotransferase; domain 2
(384)
Homologous Superfamily
:
Type I PLP-dependent aspartate aminotransferase-like (Major domain)
(384)
Human (Homo sapiens)
(18)
1a
1j04A02
A:34-282
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aspartate Aminotransferase, domain 1
(355)
Homologous Superfamily
:
Aspartate Aminotransferase, domain 1
(354)
Human (Homo sapiens)
(15)
2a
1j04A01
A:4-33,A:283-390
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Atom Selection
(currently selected atoms:
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)
Protein
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Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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