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2DW6
Biol. Unit 1
Info
Asym.Unit (258 KB)
Biol.Unit 1 (129 KB)
Biol.Unit 2 (129 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE MUTANT K184A OF D-TARTRATE DEHYDRATASE FROM BRADYRHIZOBIUM JAPONICUM COMPLEXED WITH MG++ AND D-TARTRATE
Authors
:
A. A. Fedorov, E. V. Fedorov, W. S. Yew, B. M. Wood, J. A. Gerlt, S. C. Almo
Date
:
07 Aug 06 (Deposition) - 19 Dec 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
D-Tartrate Dehydratase, Enolase Superfamily, D-Tartrate, L- Tartrate, Lyase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
W. S. Yew, A. A. Fedorov, E. V. Fedorov, B. M. Wood, S. C. Almo, J. A. Gerlt
Evolution Of Enzymatic Activities In The Enolase Superfamily: D-Tartrate Dehydratase From Bradyrhizobium Japonicum
Biochemistry V. 45 14598 2006
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
2a: D(-)-TARTARIC ACID (TARa)
2b: D(-)-TARTARIC ACID (TARb)
2c: D(-)-TARTARIC ACID (TARc)
3a: L(+)-TARTARIC ACID (TLAa)
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No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
TAR
2
Ligand/Ion
D(-)-TARTARIC ACID
3
TLA
-1
Ligand/Ion
L(+)-TARTARIC ACID
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC6 (SOFTWARE)
4: AC7 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:213 , GLU A:239 , GLU A:265 , TAR A:1001 , HOH A:2002
BINDING SITE FOR RESIDUE MG A 2001
2
AC2
SOFTWARE
ASP B:213 , GLU B:239 , GLU B:265 , TAR B:1002 , HOH B:2003
BINDING SITE FOR RESIDUE MG B 2002
3
AC6
SOFTWARE
ASN A:21 , PHE A:26 , ASN A:55 , TYR A:156 , LYS A:182 , ASP A:213 , ASN A:215 , GLU A:239 , GLU A:265 , HIS A:322 , GLU A:341 , TYR A:343 , MG A:2001 , HOH A:2002 , LYS B:102
BINDING SITE FOR RESIDUE TAR A 1001
4
AC7
SOFTWARE
LYS A:102 , ASN B:21 , PHE B:26 , ASN B:55 , TYR B:156 , LYS B:182 , ASP B:213 , ASN B:215 , GLU B:239 , GLU B:265 , HIS B:322 , GLU B:341 , TYR B:343 , MG B:2002 , HOH B:2003 , HOH B:2073
BINDING SITE FOR RESIDUE TAR B 1002
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Exons
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2dw6a2 (A:2-142)
1b: SCOP_d2dw6b2 (B:2-142)
1c: SCOP_d2dw6c2 (C:2-142)
1d: SCOP_d2dw6d2 (D:2-142)
2a: SCOP_d2dw6a1 (A:143-389)
2b: SCOP_d2dw6b1 (B:143-389)
2c: SCOP_d2dw6c1 (C:143-389)
2d: SCOP_d2dw6d1 (D:143-389)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Enolase N-terminal domain-like
(211)
Superfamily
:
Enolase N-terminal domain-like
(211)
Family
:
automated matches
(123)
Protein domain
:
automated matches
(123)
Bradyrhizobium japonicum [TaxId: 375]
(2)
1a
d2dw6a2
A:2-142
1b
d2dw6b2
B:2-142
1c
d2dw6c2
C:2-142
1d
d2dw6d2
D:2-142
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Enolase C-terminal domain-like
(212)
Family
:
D-glucarate dehydratase-like
(65)
Protein domain
:
automated matches
(16)
Bradyrhizobium japonicum [TaxId: 375]
(2)
2a
d2dw6a1
A:143-389
2b
d2dw6b1
B:143-389
2c
d2dw6c1
C:143-389
2d
d2dw6d1
D:143-389
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2dw6A01 (A:2-129)
1b: CATH_2dw6B01 (B:2-129)
1c: CATH_2dw6C01 (C:2-129)
1d: CATH_2dw6D01 (D:2-129)
2a: CATH_2dw6A02 (A:130-389)
2b: CATH_2dw6B02 (B:130-389)
2c: CATH_2dw6C02 (C:130-389)
2d: CATH_2dw6D02 (D:130-389)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Enolase-like; domain 1
(252)
Homologous Superfamily
:
Enolase-like, N-terminal domain
(130)
Bradyrhizobium japonicum. Organism_taxid: 375.
(3)
1a
2dw6A01
A:2-129
1b
2dw6B01
B:2-129
1c
2dw6C01
C:2-129
1d
2dw6D01
D:2-129
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Enolase superfamily
(142)
Bradyrhizobium japonicum. Organism_taxid: 375.
(3)
2a
2dw6A02
A:130-389
2b
2dw6B02
B:130-389
2c
2dw6C02
C:130-389
2d
2dw6D02
D:130-389
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (258 KB)
Header - Asym.Unit
Biol.Unit 1 (129 KB)
Header - Biol.Unit 1
Biol.Unit 2 (129 KB)
Header - Biol.Unit 2
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