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1ON9
Biol. Unit 1
Info
Asym.Unit (547 KB)
Biol.Unit 1 (539 KB)
Biol.Unit 2 (539 KB)
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(1)
Title
:
TRANSCARBOXYLASE 12S CRYSTAL STRUCTURE: HEXAMER ASSEMBLY AND SUBSTRATE BINDING TO A MULTIENZYME CORE (WITH HYDROLYZED METHYLMALONYL-COENZYME A BOUND)
Authors
:
P. R. Hall, Y. -F. Wang, R. E. Rivera-Hainaj, X. Zheng, M. Pustai-Carey, P. R. Carey, V. C. Yee
Date
:
27 Feb 03 (Deposition) - 20 May 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: D,E,F (2x)
Keywords
:
Carboxyl Transferase, Domain Duplication, Multienzyme Complex, Transcarboxylase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. R. Hall, Y. -F. Wang, R. E. Rivera-Hainaj, X. Zheng, M. Pustai-Carey P. R. Carey, V. C. Yee
Transcarboxylase 12S Crystal Structure: Hexamer Assembly An Substrate Binding To A Multienzyme Core
Embo J. V. 22 2334 2003
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Hetero Components
(2, 7)
Info
All Hetero Components
1a: CADMIUM ION (CDa)
1b: CADMIUM ION (CDb)
1c: CADMIUM ION (CDc)
2a: METHYLMALONYL-COENZYME A (MCAa)
2b: METHYLMALONYL-COENZYME A (MCAb)
2c: METHYLMALONYL-COENZYME A (MCAc)
2d: METHYLMALONYL-COENZYME A (MCAd)
2e: METHYLMALONYL-COENZYME A (MCAe)
2f: METHYLMALONYL-COENZYME A (MCAf)
3a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CD
-1
Ligand/Ion
CADMIUM ION
2
MCA
6
Ligand/Ion
METHYLMALONYL-COENZYME A
3
MPD
1
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
[
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Sites
(10, 10)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:388 , HOH A:7006 , HOH A:7009 , HOH A:7407 , HIS D:388 , HOH D:4368
BINDING SITE FOR RESIDUE CD A 7001
02
AC2
SOFTWARE
HIS B:388 , HOH B:7010 , HOH B:7252 , HIS E:388 , HOH E:4466 , HOH E:4468
BINDING SITE FOR RESIDUE CD B 7002
03
AC3
SOFTWARE
HIS C:388 , HOH C:7009 , HOH C:7010 , HIS F:388 , HOH F:6008 , HOH F:6258
BINDING SITE FOR RESIDUE CD C 7003
04
AC4
SOFTWARE
ARG A:34 , ARG A:35 , PHE A:105 , MET A:108 , GLY A:109 , SER A:111 , GLY A:141 , ALA A:143 , HOH A:7158 , HOH A:7535
BINDING SITE FOR RESIDUE MCA A 4001
05
AC5
SOFTWARE
ARG B:35 , MET B:108 , GLY B:109 , SER B:111 , ALA B:143 , HOH B:7215 , HOH B:7351 , HOH B:7359 , HOH B:7416 , HOH B:7499
BINDING SITE FOR RESIDUE MCA B 4002
06
AC6
SOFTWARE
ARG C:34 , ARG C:35 , LYS C:38 , PHE C:105 , MET C:108 , GLY C:109 , SER C:111 , GLY C:141 , ALA C:143 , HOH C:7148 , HOH C:7494 , HOH C:7535
BINDING SITE FOR RESIDUE MCA C 4003
07
AC7
SOFTWARE
ARG D:34 , ARG D:35 , LYS D:38 , PHE D:105 , MET D:108 , GLY D:109 , SER D:111 , GLY D:141 , ALA D:143 , HOH D:4240 , HOH D:4282 , HOH D:4361
BINDING SITE FOR RESIDUE MCA D 4004
08
AC8
SOFTWARE
HOH A:7494 , ARG E:34 , ARG E:35 , LYS E:38 , MET E:108 , GLY E:109 , SER E:111 , GLY E:141 , ALA E:143 , HOH E:4140 , HOH E:4384 , HOH E:4494 , HOH E:4515
BINDING SITE FOR RESIDUE MCA E 4005
09
AC9
SOFTWARE
ARG F:34 , ARG F:35 , LYS F:38 , PHE F:105 , MET F:108 , GLY F:109 , SER F:111 , GLY F:141 , ALA F:143 , HOH F:6104 , HOH F:6416 , HOH F:6442 , HOH F:6537
BINDING SITE FOR RESIDUE MCA F 4006
10
BC1
SOFTWARE
LYS F:251 , ASN F:268 , TRP F:303 , ASP F:305 , HOH F:6246 , HOH F:6270 , HOH F:6284 , HOH F:6546 , HOH F:6563
BINDING SITE FOR RESIDUE MPD F 6006
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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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PROSITE Patterns/Profiles
(2, 12)
Info
All PROSITE Patterns/Profiles
1: COA_CT_NTER (A:13-268,B:13-268,C:13-268,D:13-26...)
2: COA_CT_CTER (A:274-506,B:274-506,C:274-506,D:27...)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COA_CT_NTER
PS50980
Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile.
12S_PROFR
13-268
6
A:13-268
B:13-268
C:13-268
D:13-268
E:13-268
F:13-268
2
COA_CT_CTER
PS50989
Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile.
12S_PROFR
274-506
6
A:274-506
B:274-506
C:274-506
D:274-506
E:274-506
F:274-506
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d1on9a1 (A:9-260)
1b: SCOP_d1on9a2 (A:261-524)
1c: SCOP_d1on9b1 (B:9-260)
1d: SCOP_d1on9b2 (B:261-524)
1e: SCOP_d1on9c1 (C:8-260)
1f: SCOP_d1on9c2 (C:261-524)
1g: SCOP_d1on9d1 (D:7-260)
1h: SCOP_d1on9d2 (D:261-524)
1i: SCOP_d1on9e1 (E:6-260)
1j: SCOP_d1on9e2 (E:261-524)
1k: SCOP_d1on9f1 (F:9-260)
1l: SCOP_d1on9f2 (F:261-524)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
ClpP/crotonase
(207)
Superfamily
:
ClpP/crotonase
(207)
Family
:
Biotin dependent carboxylase carboxyltransferase domain
(32)
Protein domain
:
Methylmalonyl-CoA carboxyltransferase (transcarboxylase 12S)
(2)
Propionibacterium freudenreichii [TaxId: 1744]
(2)
1a
d1on9a1
A:9-260
1b
d1on9a2
A:261-524
1c
d1on9b1
B:9-260
1d
d1on9b2
B:261-524
1e
d1on9c1
C:8-260
1f
d1on9c2
C:261-524
1g
d1on9d1
D:7-260
1h
d1on9d2
D:261-524
1i
d1on9e1
E:6-260
1j
d1on9e2
E:261-524
1k
d1on9f1
F:9-260
1l
d1on9f2
F:261-524
[
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CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_1on9D02 (D:273-524)
1b: CATH_1on9F02 (F:273-524)
1c: CATH_1on9A01 (A:9-262)
1d: CATH_1on9B01 (B:9-262)
1e: CATH_1on9F01 (F:9-262)
1f: CATH_1on9C01 (C:8-262)
1g: CATH_1on9D01 (D:7-262)
1h: CATH_1on9E01 (E:6-262)
1i: CATH_1on9C02 (C:273-524)
1j: CATH_1on9A02 (A:273-524)
1k: CATH_1on9B02 (B:273-524)
1l: CATH_1on9E02 (E:273-524)
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)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
2-enoyl-CoA Hydratase; Chain A, domain 1
(89)
Homologous Superfamily
:
2-enoyl-CoA Hydratase; Chain A, domain 1
(89)
Propionibacterium freudenreichii. Organism_taxid: 1744.
(2)
1a
1on9D02
D:273-524
1b
1on9F02
F:273-524
1c
1on9A01
A:9-262
1d
1on9B01
B:9-262
1e
1on9F01
F:9-262
1f
1on9C01
C:8-262
1g
1on9D01
D:7-262
1h
1on9E01
E:6-262
1i
1on9C02
C:273-524
1j
1on9A02
A:273-524
1k
1on9B02
B:273-524
1l
1on9E02
E:273-524
[
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Carboxyl_trans_1on9F01 (F:38-518)
1b: PFAM_Carboxyl_trans_1on9F02 (F:38-518)
1c: PFAM_Carboxyl_trans_1on9F03 (F:38-518)
1d: PFAM_Carboxyl_trans_1on9F04 (F:38-518)
1e: PFAM_Carboxyl_trans_1on9F05 (F:38-518)
1f: PFAM_Carboxyl_trans_1on9F06 (F:38-518)
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)
Clan
:
ClpP_crotonase
(88)
Family
:
Carboxyl_trans
(13)
Propionibacterium freudenreichii subsp. shermanii
(2)
1a
Carboxyl_trans-1on9F01
F:38-518
1b
Carboxyl_trans-1on9F02
F:38-518
1c
Carboxyl_trans-1on9F03
F:38-518
1d
Carboxyl_trans-1on9F04
F:38-518
1e
Carboxyl_trans-1on9F05
F:38-518
1f
Carboxyl_trans-1on9F06
F:38-518
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Asymmetric Unit 1
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