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1X9J
Biol. Unit 1
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
(3, 14)
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 only available for the asymmetric unit)
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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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.
(no "Exon" information available for biological units yet)
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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)
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)
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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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Sorry, no Info available
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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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Clans
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(
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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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