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Asym. Unit
Info
Asym.Unit (397 KB)
Biol.Unit 1 (199 KB)
Biol.Unit 2 (194 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF METHYLMALONIC ACIDEMIA TYPE A PROTEIN
Authors
:
J. R. C. Muniz, C. Gileadi, D. S. Froese, W. W. Yue, A. C. W. Pike, F. Von Delft, G. Kochan, R. Sethi, A. Chaikuad, E. Pilka, S. Picaud, C. Phillips, K. Guo, E. Krysztofinska, J. Bray, N. Burgess-Brown, C. H. Arrowsmith, J. Weigelt, A. Edwards, C. Bountra, R. A. Gravel, K. L. Kavanagh, U. Oppermann
Date
:
30 Oct 09 (Deposition) - 17 Nov 09 (Release) - 27 Nov 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.64
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: C,D (1x)
Biol. Unit 2: A,B (1x)
Keywords
:
Transport Protein, Nucleotide-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. S. Froese, G. Kochan, J. R. C. Muniz, X. Wu, C. Gileadi, E. Ugochukwu, E. Krysztofinska, R. A. Gravel, U. Oppermann, W. W. Yue
Structures Of The Human Gtpase Mmaa And Vitamin B12-Dependent Methylmalonyl-Coa Mutase And Insight Into Their Complex Formation.
J. Biol. Chem. V. 285 38204 2010
[
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Hetero Components
(2, 7)
Info
All Hetero Components
1a: NONAETHYLENE GLYCOL (2PEa)
1b: NONAETHYLENE GLYCOL (2PEb)
1c: NONAETHYLENE GLYCOL (2PEc)
2a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
2b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
2c: GUANOSINE-5'-DIPHOSPHATE (GDPc)
2d: GUANOSINE-5'-DIPHOSPHATE (GDPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2PE
3
Ligand/Ion
NONAETHYLENE GLYCOL
2
GDP
4
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
[
close Hetero Component info
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PRO A:141 , ALA A:143 , ASP A:237 , ASP A:258 , GLN A:346 , LEU A:355
BINDING SITE FOR RESIDUE 2PE A 500
2
AC2
SOFTWARE
GLY A:153 , ALA A:154 , GLY A:155 , LYS A:156 , SER A:157 , THR A:158 , LYS A:290 , ASP A:292 , SER A:328 , ALA A:329 , ARG A:330 , HOH A:2012
BINDING SITE FOR RESIDUE GDP A 600
3
AC3
SOFTWARE
PRO B:151 , GLY B:153 , ALA B:154 , GLY B:155 , LYS B:156 , SER B:157 , THR B:158 , ASP B:292 , SER B:328 , ALA B:329 , ARG B:330 , HOH B:2020
BINDING SITE FOR RESIDUE GDP B 600
4
AC4
SOFTWARE
PRO C:141 , ALA C:143 , PHE C:144 , ARG C:170 , GLY C:171 , HIS C:172 , ASP C:237 , GLN C:346
BINDING SITE FOR RESIDUE 2PE C 500
5
AC5
SOFTWARE
GLY C:153 , ALA C:154 , GLY C:155 , LYS C:156 , SER C:157 , THR C:158 , LYS C:290 , ASP C:292 , SER C:328 , ALA C:329 , ARG C:330 , HOH C:2014 , HOH C:2015
BINDING SITE FOR RESIDUE GDP C 600
6
AC6
SOFTWARE
GLU D:82 , PRO D:141 , PHE D:144 , ARG D:170 , HIS D:172 , ASP D:237 , GLN D:346 , HOH D:2028
BINDING SITE FOR RESIDUE 2PE D 500
7
AC7
SOFTWARE
GLY D:153 , ALA D:154 , GLY D:155 , LYS D:156 , SER D:157 , THR D:158 , LYS D:290 , ASP D:292 , SER D:328 , ALA D:329 , ARG D:330 , HOH D:2029 , HOH D:2030
BINDING SITE FOR RESIDUE GDP D 600
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SAPs(SNPs)/Variants
(9, 33)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_020835 (L89P, chain A/B/C/D, )
2: VAR_020836 (R145Q, chain A/B/C/D, )
3: VAR_017202 (Y207C, chain A/B/C/D, )
4: VAR_071919 (R209S, chain A/B/C/D, )
5: VAR_071920 (E250K, chain A/B/C/D, )
6: VAR_071923 (K276E, chain D, )
7: VAR_038804 (R359G, chain A/B/C/D, )
8: VAR_020838 (R359Q, chain A/B/C/D, )
9: VAR_020423 (Q363H, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_020835
L
89
P
MMAA_HUMAN
Disease (MMAA)
---
A/B/C/D
L
89
P
2
UniProt
VAR_020836
R
145
Q
MMAA_HUMAN
Disease (MMAA)
200577967
A/B/C/D
R
145
Q
3
UniProt
VAR_017202
Y
207
C
MMAA_HUMAN
Disease (MMAA)
---
A/B/C/D
Y
207
C
4
UniProt
VAR_071919
R
209
S
MMAA_HUMAN
Disease (MMAA)
---
A/B/C/D
R
209
S
5
UniProt
VAR_071920
E
250
K
MMAA_HUMAN
Disease (MMAA)
---
A/B/C/D
E
250
K
6
UniProt
VAR_071923
K
276
E
MMAA_HUMAN
Disease (MMAA)
---
D
K
276
E
7
UniProt
VAR_038804
R
359
G
MMAA_HUMAN
Disease (MMAA)
---
A/B/C/D
R
359
G
8
UniProt
VAR_020838
R
359
Q
MMAA_HUMAN
Disease (MMAA)
---
A/B/C/D
R
359
Q
9
UniProt
VAR_020423
Q
363
H
MMAA_HUMAN
Polymorphism
2270655
A/B/C/D
Q
363
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2wwwa_ (A:)
1b: SCOP_d2wwwb_ (B:)
1c: SCOP_d2wwwc_ (C:)
1d: SCOP_d2wwwd_ (D:)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
automated matches
(303)
Protein domain
:
automated matches
(303)
Human (Homo sapiens) [TaxId: 9606]
(86)
1a
d2wwwa_
A:
1b
d2wwwb_
B:
1c
d2wwwc_
C:
1d
d2wwwd_
D:
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2wwwD02 (D:136-351)
1b: CATH_2wwwB02 (B:136-351)
1c: CATH_2wwwC02 (C:136-351)
1d: CATH_2wwwA02 (A:136-351)
2a: CATH_2wwwC01 (C:84-135)
2b: CATH_2wwwB01 (B:77-135)
2c: CATH_2wwwA01 (A:75-135)
2d: CATH_2wwwD01 (D:73-135)
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(
)
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Human (Homo sapiens)
(413)
1a
2wwwD02
D:136-351
1b
2wwwB02
B:136-351
1c
2wwwC02
C:136-351
1d
2wwwA02
A:136-351
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
[code=1.20.5.170, no name defined]
(60)
Human (Homo sapiens)
(20)
2a
2wwwC01
C:84-135
2b
2wwwB01
B:77-135
2c
2wwwA01
A:75-135
2d
2wwwD01
D:73-135
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_ArgK_2wwwD01 (D:101-384)
1b: PFAM_ArgK_2wwwD02 (D:101-384)
1c: PFAM_ArgK_2wwwD03 (D:101-384)
1d: PFAM_ArgK_2wwwD04 (D:101-384)
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Organisms
(
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(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
ArgK
(7)
Homo sapiens (Human)
(1)
1a
ArgK-2wwwD01
D:101-384
1b
ArgK-2wwwD02
D:101-384
1c
ArgK-2wwwD03
D:101-384
1d
ArgK-2wwwD04
D:101-384
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Asym.Unit (397 KB)
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