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2R0N
Biol. Unit 1
Info
Asym.Unit (72 KB)
Biol.Unit 1 (67 KB)
Biol.Unit 2 (261 KB)
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(1)
Title
:
THE EFFECT OF A GLU370ASP MUTATION IN GLUTARYL-COA DEHYDROGENASE ON PROTON TRANSFER TO THE DIENOLATE INTERMEDIATE
Authors
:
K. S. Rao, M. Albro, Z. Fu, B. Narayanan, S. Baddam, H. J. Lee, J. J. Kim, F. E. Frerman
Date
:
20 Aug 07 (Deposition) - 22 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Biol. Unit 2: A (4x)
Keywords
:
Glutaryl-Coa Dehydrogenase, Flavoprotein, Isomerase, Alternative Splicing, Disease Mutation, Fad, Mitochondrion, Oxidoreductase, Polymorphism, Transit Peptide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. S. Rao, Z. Fu, M. Albro, B. Narayanan, S. Baddam, H. J. Lee, J. J. Kim, F. E. Frerman
The Effect Of A Glu370Asp Mutation In Glutaryl-Coa Dehydrogenase On Proton Transfer To The Dienolate Intermediate.
Biochemistry V. 46 14468 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2a: 3-THIAGLUTARYL-COA (TGCa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
TGC
1
Ligand/Ion
3-THIAGLUTARYL-COA
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PHE A:133 , LEU A:135 , THR A:136 , GLY A:141 , SER A:142 , TRP A:168 , ILE A:169 , THR A:170 , LEU A:212 , ARG A:275 , PHE A:278 , ASN A:285 , GLN A:286 , ASP A:343 , MET A:344 , GLY A:347 , ILE A:350 , TYR A:369 , GLU A:370 , THR A:372 , ASP A:374 , PHE A:390 , HOH A:502 , HOH A:505 , HOH A:510 , HOH A:521 , HOH A:551
BINDING SITE FOR RESIDUE FAD A 400
2
AC2
SOFTWARE
ARG A:94 , SER A:95 , SER A:98 , GLY A:141 , SER A:142 , PRO A:144 , GLY A:240 , PHE A:243 , LEU A:246 , ASN A:247 , ARG A:250 , PRO A:320 , TYR A:369 , GLU A:370 , ILE A:379 , ARG A:382 , PHE A:390 , HOH A:503 , HOH A:537 , HOH A:584 , HOH A:594
BINDING SITE FOR RESIDUE TGC A 500
[
close Site info
]
SAPs(SNPs)/Variants
(60, 60)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_071510 (E20D, chain A, )
02: VAR_000366 (R44C, chain A, )
03: VAR_000367 (R50L, chain A, )
04: VAR_000368 (G57R, chain A, )
05: VAR_000369 (C71Y, chain A, )
06: VAR_000370 (A78V, chain A, )
07: VAR_000371 (R84G, chain A, )
08: VAR_000372 (R94G, chain A, )
09: VAR_000373 (S95L, chain A, )
10: VAR_000374 (V104I, chain A, )
11: VAR_000375 (R117Q, chain A, )
12: VAR_000376 (G134R, chain A, )
13: VAR_000377 (L135R, chain A, )
14: VAR_000378 (M147T, chain A, )
15: VAR_000379 (A151T, chain A, )
16: VAR_000380 (R183P, chain A, )
17: VAR_000381 (F192L, chain A, )
18: VAR_000382 (R213Q, chain A, )
19: VAR_000383 (R213W, chain A, )
20: VAR_060588 (M219V, chain A, )
21: VAR_000384 (M222V, chain A, )
22: VAR_071511 (G224V, chain A, )
23: VAR_000385 (P234S, chain A, )
24: VAR_000386 (L239P, chain A, )
25: VAR_000387 (A249T, chain A, )
26: VAR_000388 (R250W, chain A, )
27: VAR_000389 (Y251H, chain A, )
28: VAR_000390 (A254T, chain A, )
29: VAR_000391 (A254V, chain A, )
30: VAR_000392 (S261L, chain A, )
31: VAR_000393 (C264S, chain A, )
32: VAR_000394 (L265W, chain A, )
33: VAR_000395 (R269W, chain A, )
34: VAR_000396 (Q289E, chain A, )
35: VAR_000397 (A305T, chain A, )
36: VAR_000398 (G310R, chain A, )
37: VAR_000399 (G310S, chain A, )
38: VAR_000400 (R311C, chain A, )
39: VAR_000401 (R311H, chain A, )
40: VAR_000402 (E321K, chain A, )
41: VAR_000403 (C331R, chain A, )
42: VAR_000404 (A338T, chain A, )
43: VAR_000405 (R339C, chain A, )
44: VAR_000406 (R339H, chain A, )
45: VAR_000407 (R342Q, chain A, )
46: VAR_000409 (G346A, chain A, )
47: VAR_000408 (G346R, chain A, )
48: VAR_000410 (N348D, chain A, )
49: VAR_000411 (V356M, chain A, )
50: VAR_000413 (R358Q, chain A, )
51: VAR_000412 (R358W, chain A, )
52: VAR_000414 (H359R, chain A, )
53: VAR_000415 (N362K, chain A, )
54: VAR_000416 (L363P, chain A, )
55: VAR_000417 (E370K, chain A, )
56: VAR_000418 (T372I, chain A, )
57: VAR_000419 (A377T, chain A, )
58: VAR_000420 (A377V, chain A, )
59: VAR_000421 (T385M, chain A, )
60: VAR_000422 (A389E, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_071510
E
64
D
GCDH_HUMAN
Disease (GA1)
---
A
E
20
D
02
UniProt
VAR_000366
R
88
C
GCDH_HUMAN
Disease (GA1)
---
A
R
44
C
03
UniProt
VAR_000367
R
94
L
GCDH_HUMAN
Disease (GA1)
---
A
R
50
L
04
UniProt
VAR_000368
G
101
R
GCDH_HUMAN
Disease (GA1)
---
A
G
57
R
05
UniProt
VAR_000369
C
115
Y
GCDH_HUMAN
Disease (GA1)
---
A
C
71
Y
06
UniProt
VAR_000370
A
122
V
GCDH_HUMAN
Disease (GA1)
---
A
A
78
V
07
UniProt
VAR_000371
R
128
G
GCDH_HUMAN
Disease (GA1)
---
A
R
84
G
08
UniProt
VAR_000372
R
138
G
GCDH_HUMAN
Disease (GA1)
---
A
R
94
G
09
UniProt
VAR_000373
S
139
L
GCDH_HUMAN
Disease (GA1)
---
A
S
95
L
10
UniProt
VAR_000374
V
148
I
GCDH_HUMAN
Disease (GA1)
---
A
V
104
I
11
UniProt
VAR_000375
R
161
Q
GCDH_HUMAN
Disease (GA1)
---
A
R
117
Q
12
UniProt
VAR_000376
G
178
R
GCDH_HUMAN
Disease (GA1)
---
A
G
134
R
13
UniProt
VAR_000377
L
179
R
GCDH_HUMAN
Disease (GA1)
---
A
L
135
R
14
UniProt
VAR_000378
M
191
T
GCDH_HUMAN
Disease (GA1)
---
A
M
147
T
15
UniProt
VAR_000379
A
195
T
GCDH_HUMAN
Disease (GA1)
---
A
A
151
T
16
UniProt
VAR_000380
R
227
P
GCDH_HUMAN
Disease (GA1)
---
A
R
183
P
17
UniProt
VAR_000381
F
236
L
GCDH_HUMAN
Disease (GA1)
---
A
F
192
L
18
UniProt
VAR_000382
R
257
Q
GCDH_HUMAN
Disease (GA1)
---
A
R
213
Q
19
UniProt
VAR_000383
R
257
W
GCDH_HUMAN
Disease (GA1)
---
A
R
213
W
20
UniProt
VAR_060588
M
263
V
GCDH_HUMAN
Disease (GA1)
---
A
M
219
V
21
UniProt
VAR_000384
M
266
V
GCDH_HUMAN
Disease (GA1)
---
A
M
222
V
22
UniProt
VAR_071511
G
268
V
GCDH_HUMAN
Disease (GA1)
---
A
G
224
V
23
UniProt
VAR_000385
P
278
S
GCDH_HUMAN
Disease (GA1)
---
A
P
234
S
24
UniProt
VAR_000386
L
283
P
GCDH_HUMAN
Disease (GA1)
---
A
L
239
P
25
UniProt
VAR_000387
A
293
T
GCDH_HUMAN
Disease (GA1)
---
A
A
249
T
26
UniProt
VAR_000388
R
294
W
GCDH_HUMAN
Disease (GA1)
---
A
R
250
W
27
UniProt
VAR_000389
Y
295
H
GCDH_HUMAN
Disease (GA1)
---
A
Y
251
H
28
UniProt
VAR_000390
A
298
T
GCDH_HUMAN
Polymorphism
---
A
A
254
T
29
UniProt
VAR_000391
A
298
V
GCDH_HUMAN
Polymorphism
---
A
A
254
V
30
UniProt
VAR_000392
S
305
L
GCDH_HUMAN
Disease (GA1)
---
A
S
261
L
31
UniProt
VAR_000393
C
308
S
GCDH_HUMAN
Disease (GA1)
---
A
C
264
S
32
UniProt
VAR_000394
L
309
W
GCDH_HUMAN
Disease (GA1)
---
A
L
265
W
33
UniProt
VAR_000395
R
313
W
GCDH_HUMAN
Disease (GA1)
---
A
R
269
W
34
UniProt
VAR_000396
Q
333
E
GCDH_HUMAN
Disease (GA1)
---
A
Q
289
E
35
UniProt
VAR_000397
A
349
T
GCDH_HUMAN
Disease (GA1)
---
A
A
305
T
36
UniProt
VAR_000398
G
354
R
GCDH_HUMAN
Disease (GA1)
---
A
G
310
R
37
UniProt
VAR_000399
G
354
S
GCDH_HUMAN
Disease (GA1)
---
A
G
310
S
38
UniProt
VAR_000400
R
355
C
GCDH_HUMAN
Disease (GA1)
---
A
R
311
C
39
UniProt
VAR_000401
R
355
H
GCDH_HUMAN
Disease (GA1)
---
A
R
311
H
40
UniProt
VAR_000402
E
365
K
GCDH_HUMAN
Disease (GA1)
---
A
E
321
K
41
UniProt
VAR_000403
C
375
R
GCDH_HUMAN
Disease (GA1)
---
A
C
331
R
42
UniProt
VAR_000404
A
382
T
GCDH_HUMAN
Disease (GA1)
---
A
A
338
T
43
UniProt
VAR_000405
R
383
C
GCDH_HUMAN
Disease (GA1)
---
A
R
339
C
44
UniProt
VAR_000406
R
383
H
GCDH_HUMAN
Disease (GA1)
---
A
R
339
H
45
UniProt
VAR_000407
R
386
Q
GCDH_HUMAN
Disease (GA1)
---
A
R
342
Q
46
UniProt
VAR_000409
G
390
A
GCDH_HUMAN
Disease (GA1)
---
A
G
346
A
47
UniProt
VAR_000408
G
390
R
GCDH_HUMAN
Disease (GA1)
---
A
G
346
R
48
UniProt
VAR_000410
N
392
D
GCDH_HUMAN
Disease (GA1)
---
A
N
348
D
49
UniProt
VAR_000411
V
400
M
GCDH_HUMAN
Disease (GA1)
---
A
V
356
M
50
UniProt
VAR_000413
R
402
Q
GCDH_HUMAN
Disease (GA1)
---
A
R
358
Q
51
UniProt
VAR_000412
R
402
W
GCDH_HUMAN
Disease (GA1)
---
A
R
358
W
52
UniProt
VAR_000414
H
403
R
GCDH_HUMAN
Disease (GA1)
---
A
H
359
R
53
UniProt
VAR_000415
N
406
K
GCDH_HUMAN
Disease (GA1)
---
A
N
362
K
54
UniProt
VAR_000416
L
407
P
GCDH_HUMAN
Disease (GA1)
---
A
L
363
P
55
UniProt
VAR_000417
E
414
K
GCDH_HUMAN
Disease (GA1)
---
A
E
370
K
56
UniProt
VAR_000418
T
416
I
GCDH_HUMAN
Disease (GA1)
---
A
T
372
I
57
UniProt
VAR_000419
A
421
T
GCDH_HUMAN
Disease (GA1)
151201155
A
A
377
T
58
UniProt
VAR_000420
A
421
V
GCDH_HUMAN
Disease (GA1)
---
A
A
377
V
59
UniProt
VAR_000421
T
429
M
GCDH_HUMAN
Disease (GA1)
---
A
T
385
M
60
UniProt
VAR_000422
A
433
E
GCDH_HUMAN
Disease (GA1)
---
A
A
389
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: ACYL_COA_DH_1 (A:134-146)
2: ACYL_COA_DH_2 (A:343-362)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ACYL_COA_DH_1
PS00072
Acyl-CoA dehydrogenases signature 1.
GCDH_HUMAN
178-190
1
A:134-146
2
ACYL_COA_DH_2
PS00073
Acyl-CoA dehydrogenases signature 2.
GCDH_HUMAN
387-406
1
A:343-362
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2r0na1 (A:239-392)
2a: SCOP_d2r0na2 (A:3-238)
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Protein Domains
(
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(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
Acyl-CoA dehydrogenase C-terminal domain-like
(61)
Family
:
Medium chain acyl-CoA dehydrogenase-like, C-terminal domain
(29)
Protein domain
:
Glutaryl-CoA dehydrogenase GCDH
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d2r0na1
A:239-392
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Acyl-CoA dehydrogenase NM domain-like
(61)
Superfamily
:
Acyl-CoA dehydrogenase NM domain-like
(61)
Family
:
Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains
(32)
Protein domain
:
Glutaryl-CoA dehydrogenase GCDH
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
2a
d2r0na2
A:3-238
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_Acyl_CoA_dh_1_2r0nA01 (A:243-385)
2a: PFAM_Acyl_CoA_dh_M_2r0nA02 (A:132-186)
3a: PFAM_Acyl_CoA_dh_N_2r0nA03 (A:17-128)
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Clans
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(
)
Families
(
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(
)
Organisms
(
)
(
)
Clan
:
Acyl-CoA_dh
(32)
Family
:
Acyl-CoA_dh_1
(24)
Homo sapiens (Human)
(10)
1a
Acyl-CoA_dh_1-2r0nA01
A:243-385
Clan
:
no clan defined [family: Acyl-CoA_dh_M]
(24)
Family
:
Acyl-CoA_dh_M
(24)
Homo sapiens (Human)
(10)
2a
Acyl-CoA_dh_M-2r0nA02
A:132-186
Clan
:
no clan defined [family: Acyl-CoA_dh_N]
(23)
Family
:
Acyl-CoA_dh_N
(23)
Homo sapiens (Human)
(10)
3a
Acyl-CoA_dh_N-2r0nA03
A:17-128
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Asym.Unit (72 KB)
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