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1X9J
Asym. Unit
Info
Asym.Unit (483 KB)
Biol.Unit 1 (477 KB)
Biol.Unit 2 (124 KB)
Biol.Unit 3 (124 KB)
Biol.Unit 4 (125 KB)
Biol.Unit 5 (125 KB)
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(1)
Title
:
STRUCTURE OF BUTYRATE KINASE 2 REVEALS BOTH OPEN- AND CITRATE-INDUCED CLOSED CONFORMATIONS: IMPLICATIONS FOR SUBSTRATE-INDUCED FIT CONFORMATIONAL CHANGES
Authors
:
J. S. Diao, D. A. Sanders, M. S. Hasson
Date
:
21 Aug 04 (Deposition) - 30 Aug 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Biol. Unit 2: A,H (1x)
Biol. Unit 3: B,C (1x)
Biol. Unit 4: F,G (1x)
Biol. Unit 5: D,E (1x)
Keywords
:
Askha (Acetate And Sugar Kinases, Hsc70, Actin) Superfamily, Butyrate Kinase, Acetate Kinase, Isobutyrate Kinase, Two Similar Domains, Butyrate, Isobutyrate, Enzyme Mechanism, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. S. Diao, S. Bhattacharyya, Y. L. D. Ma, D. A. Sanders, M. S. Hasson
Structure Of Butyrate Kinase 2 Reveals Both Open And Closed Conformations Of The Two Domains: Implications For Substrate-Induced Changes
To Be Published
(for further references see the
PDB file header
)
[
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]
Hetero Components
(4, 15)
Info
All Hetero Components
1a: CITRIC ACID (CITa)
1b: CITRIC ACID (CITb)
1c: CITRIC ACID (CITc)
1d: CITRIC ACID (CITd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
3a: SODIUM ION (NAa)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
4c: PHOSPHATE ION (PO4c)
4d: PHOSPHATE ION (PO4d)
4e: PHOSPHATE ION (PO4e)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CIT
4
Ligand/Ion
CITRIC ACID
2
GOL
5
Ligand/Ion
GLYCEROL
3
NA
1
Ligand/Ion
SODIUM ION
4
PO4
5
Ligand/Ion
PHOSPHATE ION
[
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]
Sites
(15, 15)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL D:58 , GLU D:59 , THR D:61 , TYR D:63 , GLU E:119
BINDING SITE FOR RESIDUE NA D 380
02
AC2
SOFTWARE
THR D:217 , TRP D:284 , LYS D:287 , THR E:217 , TRP E:284 , LYS E:287
BINDING SITE FOR RESIDUE PO4 E 401
03
AC3
SOFTWARE
THR B:217 , TRP B:284 , LYS B:287 , ASP C:207 , THR C:217 , TRP C:284 , LYS C:287
BINDING SITE FOR RESIDUE PO4 B 402
04
AC4
SOFTWARE
ASP F:207 , THR F:217 , TRP F:284 , LYS F:287 , THR G:217 , TRP G:284 , LYS G:287
BINDING SITE FOR RESIDUE PO4 F 403
05
AC5
SOFTWARE
ASP A:207 , THR A:217 , TRP A:284 , LYS A:287 , THR H:217 , TRP H:284 , LYS H:287
BINDING SITE FOR RESIDUE PO4 H 404
06
AC6
SOFTWARE
ARG D:55 , LYS E:97 , HIS E:114 , ARG E:115
BINDING SITE FOR RESIDUE PO4 E 405
07
AC7
SOFTWARE
SER D:11 , HIS D:104 , HIS D:154 , HIS D:182 , GLY D:184 , GLY D:185 , GLY D:186 , LEU D:204 , ARG D:214
BINDING SITE FOR RESIDUE CIT D 381
08
AC8
SOFTWARE
SER G:11 , HIS G:104 , VAL G:130 , HIS G:154 , GLY G:184 , GLY G:185 , GLY G:186 , ARG G:214 , CIT G:383
BINDING SITE FOR RESIDUE CIT G 382
09
AC9
SOFTWARE
LYS G:15 , HIS G:182 , GLY G:304 , HIS G:307 , GLY G:331 , SER G:332 , CIT G:382
BINDING SITE FOR RESIDUE CIT G 383
10
BC1
SOFTWARE
SER D:13 , LYS D:15 , ASN D:29 , GLY D:304 , GLY D:331 , SER D:332
BINDING SITE FOR RESIDUE CIT D 384
11
BC2
SOFTWARE
MET F:1 , ARG F:3 , PHE F:68
BINDING SITE FOR RESIDUE GOL F 391
12
BC3
SOFTWARE
MET C:1 , ARG C:3 , SER C:67 , PHE C:68 , SER C:69
BINDING SITE FOR RESIDUE GOL C 392
13
BC4
SOFTWARE
MET D:1 , ARG D:3 , PHE D:68 , SER D:69
BINDING SITE FOR RESIDUE GOL D 393
14
BC5
SOFTWARE
HIS B:307 , GLY B:331 , SER B:332
BINDING SITE FOR RESIDUE GOL B 394
15
BC6
SOFTWARE
VAL A:130 , HIS A:154 , ARG A:214
BINDING SITE FOR RESIDUE GOL A 395
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 16)
Info
All PROSITE Patterns/Profiles
1: ACETATE_KINASE_1 (A:4-15,B:4-15,C:4-15,D:4-15,E:4-15...)
2: ACETATE_KINASE_2 (A:178-195,B:178-195,C:178-195,D:17...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ACETATE_KINASE_1
PS01075
Acetate and butyrate kinases family signature 1.
BUK2_THEMA
4-15
8
A:4-15
B:4-15
C:4-15
D:4-15
E:4-15
F:4-15
G:4-15
H:4-15
2
ACETATE_KINASE_2
PS01076
Acetate and butyrate kinases family signature 2.
BUK2_THEMA
178-195
8
A:178-195
B:178-195
C:178-195
D:178-195
E:178-195
F:178-195
G:178-195
H:178-195
[
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]
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.
SCOP Domains
(1, 16)
Info
All SCOP Domains
1a: SCOP_d1x9ja1 (A:1-172)
1b: SCOP_d1x9je1 (E:1-172)
1c: SCOP_d1x9je2 (E:173-371)
1d: SCOP_d1x9jf1 (F:1-172)
1e: SCOP_d1x9jf2 (F:173-372)
1f: SCOP_d1x9jg1 (G:1-172)
1g: SCOP_d1x9jg2 (G:173-373)
1h: SCOP_d1x9jh1 (H:1-172)
1i: SCOP_d1x9jh2 (H:173-372)
1j: SCOP_d1x9ja2 (A:173-373)
1k: SCOP_d1x9jb1 (B:1-172)
1l: SCOP_d1x9jb2 (B:173-371)
1m: SCOP_d1x9jc1 (C:1-172)
1n: SCOP_d1x9jc2 (C:173-371)
1o: SCOP_d1x9jd1 (D:1-172)
1p: SCOP_d1x9jd2 (D:173-373)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Actin-like ATPase domain
(426)
Family
:
Acetokinase-like
(17)
Protein domain
:
butyrate kinase 2
(2)
Thermotoga maritima [TaxId: 2336]
(2)
1a
d1x9ja1
A:1-172
1b
d1x9je1
E:1-172
1c
d1x9je2
E:173-371
1d
d1x9jf1
F:1-172
1e
d1x9jf2
F:173-372
1f
d1x9jg1
G:1-172
1g
d1x9jg2
G:173-373
1h
d1x9jh1
H:1-172
1i
d1x9jh2
H:173-372
1j
d1x9ja2
A:173-373
1k
d1x9jb1
B:1-172
1l
d1x9jb2
B:173-371
1m
d1x9jc1
C:1-172
1n
d1x9jc2
C:173-371
1o
d1x9jd1
D:1-172
1p
d1x9jd2
D:173-373
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Acetate_kinase_1x9jH01 (H:3-337)
1b: PFAM_Acetate_kinase_1x9jH02 (H:3-337)
1c: PFAM_Acetate_kinase_1x9jH03 (H:3-337)
1d: PFAM_Acetate_kinase_1x9jH04 (H:3-337)
1e: PFAM_Acetate_kinase_1x9jH05 (H:3-337)
1f: PFAM_Acetate_kinase_1x9jH06 (H:3-337)
1g: PFAM_Acetate_kinase_1x9jH07 (H:3-337)
1h: PFAM_Acetate_kinase_1x9jH08 (H:3-337)
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Organisms
(
)
(
)
Clan
:
Actin_ATPase
(173)
Family
:
Acetate_kinase
(6)
Thermotoga maritima
(2)
1a
Acetate_kinase-1x9jH01
H:3-337
1b
Acetate_kinase-1x9jH02
H:3-337
1c
Acetate_kinase-1x9jH03
H:3-337
1d
Acetate_kinase-1x9jH04
H:3-337
1e
Acetate_kinase-1x9jH05
H:3-337
1f
Acetate_kinase-1x9jH06
H:3-337
1g
Acetate_kinase-1x9jH07
H:3-337
1h
Acetate_kinase-1x9jH08
H:3-337
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