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Getting 'PROSITE' information from database.
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Getting 'Exon' information from database.
3BIC
Asym. Unit
Info
Asym.Unit (222 KB)
Biol.Unit 1 (109 KB)
Biol.Unit 2 (110 KB)
Biol.Unit 3 (214 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN METHYLMALONYL-COA MUTASE
Authors
:
E. Ugochukwu, G. Kochan, N. Pantic, E. Parizotto, E. S. Pilka, A. C. W. Pi O. Gileadi, F. Von Delft, C. H. Arrowsmith, J. Weigelt, A. M. Edwards, U. Oppermann, Structural Genomics Consortium (Sgc)
Date
:
30 Nov 07 (Deposition) - 25 Dec 07 (Release) - 14 Sep 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (1x)
Keywords
:
Organic Aciduria, Methylmalonyl Coa Mutase Deficiency, Metabolic Disease, Structural Genomics, Structural Genomics Consortium, Sgc, Cobalamin, Cobalt, Disease Mutation, Isomerase, Metal-Binding, Mitochondrion, Transit Peptide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. S. Froese, G. Kochan, J. R. 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
[
close entry info
]
Hetero Components
(1, 4)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
4
Ligand/Ion
CHLORIDE ION
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:594 , LYS A:595
BINDING SITE FOR RESIDUE CL A 803
[
close Site info
]
SAPs(SNPs)/Variants
(89, 178)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_023472 (I69V, chain A/B, )
02: VAR_026592 (P86L, chain A/B, )
03: VAR_026593 (G87E, chain A/B, )
04: VAR_004409 (R93H, chain A/B, )
05: VAR_026594 (G94R, chain A/B, )
06: VAR_022393 (G94V, chain A/B, )
07: VAR_026595 (P95R, chain A/B, )
08: VAR_004410 (W105R, chain A/B, )
09: VAR_026596 (R108C, chain A/B, )
10: VAR_026597 (R108G, chain A/B, )
11: VAR_022394 (R108H, chain A/B, )
12: VAR_023473 (Q109R, chain A/B, )
13: VAR_022395 (A137V, chain A/B, )
14: VAR_026598 (G145S, chain A/B, )
15: VAR_022396 (S148L, chain A/B, )
16: VAR_022397 (D156N, chain A/B, )
17: VAR_022398 (G158V, chain A/B, )
18: VAR_022399 (F174S, chain A/B, )
19: VAR_026599 (M186V, chain A/B, )
20: VAR_026600 (N189K, chain A/B, )
21: VAR_004411 (A191E, chain A/B, )
22: VAR_026601 (A197E, chain A/B, )
23: VAR_022400 (G203R, chain A/B, )
24: VAR_026602 (G215C, chain A/B, )
25: VAR_022401 (G215S, chain A/B, )
26: VAR_022402 (Q218H, chain A/B, )
27: VAR_022403 (N219Y, chain A/B, )
28: VAR_004412 (R228Q, chain A/B, )
29: VAR_026603 (T230I, chain A/B, )
30: VAR_004413 (Y231N, chain A/B, )
31: VAR_022404 (S262N, chain A/B, )
32: VAR_026604 (H265Y, chain A/B, )
33: VAR_026605 (L281S, chain A/B, )
34: VAR_026606 (G291E, chain A/B, )
35: VAR_022405 (Q293P, chain A/B, )
36: VAR_026607 (L305S, chain A/B, )
37: VAR_026608 (S306F, chain A/B, )
38: VAR_004414 (G312V, chain A/B, )
39: VAR_026609 (Y316C, chain A/B, )
40: VAR_023474 (A324T, chain A/B, )
41: VAR_022406 (L328F, chain A/B, )
42: VAR_023475 (L328P, chain A/B, )
43: VAR_026610 (L347R, chain A/B, )
44: VAR_026611 (H350Y, chain A/B, )
45: VAR_004416 (V368D, chain A/B, )
46: VAR_026612 (R369C, chain A/B, )
47: VAR_004417 (R369H, chain A/B, )
48: VAR_026613 (T370P, chain A/B, )
49: VAR_004418 (A377E, chain A/B, )
50: VAR_026614 (Q383H, chain A/B, )
51: VAR_026615 (Q383P, chain A/B, )
52: VAR_026616 (H386N, chain A/B, )
53: VAR_026617 (N388H, chain A/B, )
54: VAR_026620 (G426R, chain A/B, )
55: VAR_026621 (G427D, chain A/B, )
56: VAR_022407 (T499T, chain A/B, )
57: VAR_026622 (L518P, chain A/B, )
58: VAR_004419 (R532H, chain A/B, )
59: VAR_022408 (A535P, chain A/B, )
60: VAR_026623 (C560Y, chain A/B, )
61: VAR_026624 (T566R, chain A/B, )
62: VAR_026625 (F573S, chain A/B, )
63: VAR_022409 (Y587C, chain A/B, )
64: VAR_030495 (T598A, chain A/B, )
65: VAR_026626 (P615R, chain A/B, )
66: VAR_022410 (P615T, chain A/B, )
67: VAR_023476 (R616C, chain A/B, )
68: VAR_023477 (L617R, chain A/B, )
69: VAR_022411 (K621N, chain A/B, )
70: VAR_004420 (G623R, chain A/B, )
71: VAR_022412 (Q624R, chain A/B, )
72: VAR_004421 (G626C, chain A/B, )
73: VAR_022413 (H627R, chain A/B, )
74: VAR_004422 (G630E, chain A/B, )
75: VAR_004423 (V633G, chain A/B, )
76: VAR_022414 (G637E, chain A/B, )
77: VAR_026627 (G637R, chain A/B, )
78: VAR_022415 (F638I, chain A/B, )
79: VAR_022416 (D640Y, chain A/B, )
80: VAR_022417 (G642R, chain A/B, )
81: VAR_004424 (G648D, chain A/B, )
82: VAR_004425 (V669E, chain A/B, )
83: VAR_004426 (V671V, chain A/B, )
84: VAR_004427 (H678R, chain A/B, )
85: VAR_004429 (L685R, chain A/B, )
86: VAR_004430 (R694W, chain A/B, )
87: VAR_022418 (M700K, chain A/B, )
88: VAR_004431 (G703R, chain A/B, )
89: VAR_004432 (G717V, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_023472
I
69
V
MUTA_HUMAN
Polymorphism
115923556
A/B
I
69
V
02
UniProt
VAR_026592
P
86
L
MUTA_HUMAN
Disease (MMAM)
---
A/B
P
86
L
03
UniProt
VAR_026593
G
87
E
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
87
E
04
UniProt
VAR_004409
R
93
H
MUTA_HUMAN
Disease (MMAM)
121918251
A/B
R
93
H
05
UniProt
VAR_026594
G
94
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
94
R
06
UniProt
VAR_022393
G
94
V
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
94
V
07
UniProt
VAR_026595
P
95
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
P
95
R
08
UniProt
VAR_004410
W
105
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
W
105
R
09
UniProt
VAR_026596
R
108
C
MUTA_HUMAN
Disease (MMAM)
121918257
A/B
R
108
C
10
UniProt
VAR_026597
R
108
G
MUTA_HUMAN
Disease (MMAM)
---
A/B
R
108
G
11
UniProt
VAR_022394
R
108
H
MUTA_HUMAN
Disease (MMAM)
---
A/B
R
108
H
12
UniProt
VAR_023473
Q
109
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
Q
109
R
13
UniProt
VAR_022395
A
137
V
MUTA_HUMAN
Disease (MMAM)
---
A/B
A
137
V
14
UniProt
VAR_026598
G
145
S
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
145
S
15
UniProt
VAR_022396
S
148
L
MUTA_HUMAN
Disease (MMAM)
---
A/B
S
148
L
16
UniProt
VAR_022397
D
156
N
MUTA_HUMAN
Disease (MMAM)
---
A/B
D
156
N
17
UniProt
VAR_022398
G
158
V
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
158
V
18
UniProt
VAR_022399
F
174
S
MUTA_HUMAN
Disease (MMAM)
---
A/B
F
174
S
19
UniProt
VAR_026599
M
186
V
MUTA_HUMAN
Disease (MMAM)
---
A/B
M
186
V
20
UniProt
VAR_026600
N
189
K
MUTA_HUMAN
Disease (MMAM)
---
A/B
N
189
K
21
UniProt
VAR_004411
A
191
E
MUTA_HUMAN
Disease (MMAM)
---
A/B
A
191
E
22
UniProt
VAR_026601
A
197
E
MUTA_HUMAN
Disease (MMAM)
---
A/B
A
197
E
23
UniProt
VAR_022400
G
203
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
203
R
24
UniProt
VAR_026602
G
215
C
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
215
C
25
UniProt
VAR_022401
G
215
S
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
215
S
26
UniProt
VAR_022402
Q
218
H
MUTA_HUMAN
Disease (MMAM)
---
A/B
Q
218
H
27
UniProt
VAR_022403
N
219
Y
MUTA_HUMAN
Disease (MMAM)
---
A/B
N
219
Y
28
UniProt
VAR_004412
R
228
Q
MUTA_HUMAN
Disease (MMAM)
---
A/B
R
228
Q
29
UniProt
VAR_026603
T
230
I
MUTA_HUMAN
Disease (MMAM)
---
A/B
T
230
I
30
UniProt
VAR_004413
Y
231
N
MUTA_HUMAN
Disease (MMAM)
---
A/B
Y
231
N
31
UniProt
VAR_022404
S
262
N
MUTA_HUMAN
Disease (MMAM)
---
A/B
S
262
N
32
UniProt
VAR_026604
H
265
Y
MUTA_HUMAN
Disease (MMAM)
---
A/B
H
265
Y
33
UniProt
VAR_026605
L
281
S
MUTA_HUMAN
Disease (MMAM)
---
A/B
L
281
S
34
UniProt
VAR_026606
G
291
E
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
291
E
35
UniProt
VAR_022405
Q
293
P
MUTA_HUMAN
Disease (MMAM)
---
A/B
Q
293
P
36
UniProt
VAR_026607
L
305
S
MUTA_HUMAN
Disease (MMAM)
---
A/B
L
305
S
37
UniProt
VAR_026608
S
306
F
MUTA_HUMAN
Disease (MMAM)
---
A/B
S
306
F
38
UniProt
VAR_004414
G
312
V
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
312
V
39
UniProt
VAR_026609
Y
316
C
MUTA_HUMAN
Disease (MMAM)
---
A/B
Y
316
C
40
UniProt
VAR_023474
A
324
T
MUTA_HUMAN
Disease (MMAM)
---
A/B
A
324
T
41
UniProt
VAR_022406
L
328
F
MUTA_HUMAN
Disease (MMAM)
---
A/B
L
328
F
42
UniProt
VAR_023475
L
328
P
MUTA_HUMAN
Disease (MMAM)
---
A/B
L
328
P
43
UniProt
VAR_026610
L
347
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
L
347
R
44
UniProt
VAR_026611
H
350
Y
MUTA_HUMAN
Disease (MMAM)
---
A/B
H
350
Y
45
UniProt
VAR_004416
V
368
D
MUTA_HUMAN
Disease (MMAM)
---
A/B
V
368
D
46
UniProt
VAR_026612
R
369
C
MUTA_HUMAN
Disease (MMAM)
---
A/B
R
369
C
47
UniProt
VAR_004417
R
369
H
MUTA_HUMAN
Disease (MMAM)
---
A/B
R
369
H
48
UniProt
VAR_026613
T
370
P
MUTA_HUMAN
Disease (MMAM)
---
A/B
T
370
P
49
UniProt
VAR_004418
A
377
E
MUTA_HUMAN
Disease (MMAM)
---
A/B
A
377
E
50
UniProt
VAR_026614
Q
383
H
MUTA_HUMAN
Disease (MMAM)
---
A/B
Q
383
H
51
UniProt
VAR_026615
Q
383
P
MUTA_HUMAN
Disease (MMAM)
---
A/B
Q
383
P
52
UniProt
VAR_026616
H
386
N
MUTA_HUMAN
Disease (MMAM)
---
A/B
H
386
N
53
UniProt
VAR_026617
N
388
H
MUTA_HUMAN
Disease (MMAM)
---
A/B
N
388
H
54
UniProt
VAR_026620
G
426
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
426
R
55
UniProt
VAR_026621
G
427
D
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
427
D
56
UniProt
VAR_022407
A
499
T
MUTA_HUMAN
Polymorphism
2229385
A/B
T
499
T
57
UniProt
VAR_026622
L
518
P
MUTA_HUMAN
Disease (MMAM)
---
A/B
L
518
P
58
UniProt
VAR_004419
R
532
H
MUTA_HUMAN
Polymorphism
1141321
A/B
R
532
H
59
UniProt
VAR_022408
A
535
P
MUTA_HUMAN
Disease (MMAM)
---
A/B
A
535
P
60
UniProt
VAR_026623
C
560
Y
MUTA_HUMAN
Disease (MMAM)
---
A/B
C
560
Y
61
UniProt
VAR_026624
T
566
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
T
566
R
62
UniProt
VAR_026625
F
573
S
MUTA_HUMAN
Disease (MMAM)
---
A/B
F
573
S
63
UniProt
VAR_022409
Y
587
C
MUTA_HUMAN
Disease (MMAM)
---
A/B
Y
587
C
64
UniProt
VAR_030495
T
598
A
MUTA_HUMAN
Polymorphism
9473556
A/B
T
598
A
65
UniProt
VAR_026626
P
615
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
P
615
R
66
UniProt
VAR_022410
P
615
T
MUTA_HUMAN
Disease (MMAM)
---
A/B
P
615
T
67
UniProt
VAR_023476
R
616
C
MUTA_HUMAN
Disease (MMAM)
---
A/B
R
616
C
68
UniProt
VAR_023477
L
617
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
L
617
R
69
UniProt
VAR_022411
K
621
N
MUTA_HUMAN
Disease (MMAM)
---
A/B
K
621
N
70
UniProt
VAR_004420
G
623
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
623
R
71
UniProt
VAR_022412
Q
624
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
Q
624
R
72
UniProt
VAR_004421
G
626
C
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
626
C
73
UniProt
VAR_022413
H
627
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
H
627
R
74
UniProt
VAR_004422
G
630
E
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
630
E
75
UniProt
VAR_004423
V
633
G
MUTA_HUMAN
Disease (MMAM)
---
A/B
V
633
G
76
UniProt
VAR_022414
G
637
E
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
637
E
77
UniProt
VAR_026627
G
637
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
637
R
78
UniProt
VAR_022415
F
638
I
MUTA_HUMAN
Disease (MMAM)
---
A/B
F
638
I
79
UniProt
VAR_022416
D
640
Y
MUTA_HUMAN
Disease (MMAM)
---
A/B
D
640
Y
80
UniProt
VAR_022417
G
642
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
642
R
81
UniProt
VAR_004424
G
648
D
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
648
D
82
UniProt
VAR_004425
V
669
E
MUTA_HUMAN
Disease (MMAM)
---
A/B
V
669
E
83
UniProt
VAR_004426
I
671
V
MUTA_HUMAN
Polymorphism
8589
A/B
V
671
V
84
UniProt
VAR_004427
H
678
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
H
678
R
85
UniProt
VAR_004429
L
685
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
L
685
R
86
UniProt
VAR_004430
R
694
W
MUTA_HUMAN
Disease (MMAM)
---
A/B
R
694
W
87
UniProt
VAR_022418
M
700
K
MUTA_HUMAN
Disease (MMAM)
---
A/B
M
700
K
88
UniProt
VAR_004431
G
703
R
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
703
R
89
UniProt
VAR_004432
G
717
V
MUTA_HUMAN
Disease (MMAM)
---
A/B
G
717
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: METMALONYL_COA_MUTASE (A:403-428,B:403-428)
2: B12_BINDING (A:614-745,B:614-746)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
METMALONYL_COA_MUTASE
PS00544
Methylmalonyl-CoA mutase signature.
MUTA_HUMAN
403-428
2
A:403-428
B:403-428
2
B12_BINDING
PS51332
B12-binding domain profile.
MUTA_HUMAN
614-746
2
A:614-745
B:614-746
[
close PROSITE info
]
Exons
(12, 24)
Info
All Exons
Exon 1.2 (A:27-128 | B:38-128)
Exon 1.3 (A:131-251 | B:131-251)
Exon 1.4 (A:252-304 | B:252-304)
Exon 1.5 (A:304-361 | B:304-361)
Exon 1.6 (A:362-444 | B:362-444)
Exon 1.7 (A:445-482 | B:445-482)
Exon 1.8 (A:482-520 (gaps) | B:482-520 (gaps...)
Exon 1.9 (A:521-559 | B:521-559)
Exon 1.10 (A:559-603 | B:559-603)
Exon 1.11 (A:603-652 | B:603-652)
Exon 1.12 (A:653-708 | B:653-708)
Exon 1.13 (A:709-745 | B:709-750)
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All Exon Boundaries
01: Boundary 1.1/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/1.11
11: Boundary 1.11/1.12
12: Boundary 1.12/1.13
13: Boundary 1.13/-
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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
1.1
ENST00000274813
1
ENSE00001926852
chr6:
49430904-49430816
89
MUTA_HUMAN
-
0
0
-
-
1.2
ENST00000274813
2
ENSE00001167247
chr6:
49427218-49426795
424
MUTA_HUMAN
1-129
129
2
A:27-128
B:38-128
102
91
1.3
ENST00000274813
3
ENSE00000973845
chr6:
49425771-49425404
368
MUTA_HUMAN
129-251
123
2
A:131-251
B:131-251
121
121
1.4
ENST00000274813
4
ENSE00001139050
chr6:
49423950-49423793
158
MUTA_HUMAN
252-304
53
2
A:252-304
B:252-304
53
53
1.5
ENST00000274813
5
ENSE00001139044
chr6:
49421469-49421298
172
MUTA_HUMAN
304-361
58
2
A:304-361
B:304-361
58
58
1.6
ENST00000274813
6
ENSE00001139037
chr6:
49419427-49419179
249
MUTA_HUMAN
362-444
83
2
A:362-444
B:362-444
83
83
1.7
ENST00000274813
7
ENSE00001139030
chr6:
49416640-49416529
112
MUTA_HUMAN
445-482
38
2
A:445-482
B:445-482
38
38
1.8
ENST00000274813
8
ENSE00001139024
chr6:
49415498-49415383
116
MUTA_HUMAN
482-520
39
2
A:482-520 (gaps)
B:482-520 (gaps)
39
39
1.9
ENST00000274813
9
ENSE00000973851
chr6:
49412467-49412352
116
MUTA_HUMAN
521-559
39
2
A:521-559
B:521-559
39
39
1.10
ENST00000274813
10
ENSE00000973852
chr6:
49409684-49409553
132
MUTA_HUMAN
559-603
45
2
A:559-603
B:559-603
45
45
1.11
ENST00000274813
11
ENSE00001139009
chr6:
49408066-49407919
148
MUTA_HUMAN
603-652
50
2
A:603-652
B:603-652
50
50
1.12
ENST00000274813
12
ENSE00000973854
chr6:
49403336-49403169
168
MUTA_HUMAN
653-708
56
2
A:653-708
B:653-708
56
56
1.13
ENST00000274813
13
ENSE00000973855
chr6:
49399569-49398073
1497
MUTA_HUMAN
709-750
42
2
A:709-745
B:709-750
37
42
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SCOP Domains
(0, 0)
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CATH Domains
(2, 4)
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all CATH domains
1a: CATH_3bicA02 (A:580-743)
1b: CATH_3bicB02 (B:580-757)
2a: CATH_3bicA01 (A:61-576)
2b: CATH_3bicB01 (B:38-576)
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Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.280, no name defined]
(23)
Human (Homo sapiens)
(1)
1a
3bicA02
A:580-743
1b
3bicB02
B:580-757
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
[code=3.20.20.240, no name defined]
(12)
Human (Homo sapiens)
(1)
2a
3bicA01
A:61-576
2b
3bicB01
B:38-576
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Pfam Domains
(0, 0)
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