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2DKB
Biol. Unit 2
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Asym.Unit (79 KB)
Biol.Unit 1 (142 KB)
Biol.Unit 2 (282 KB)
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(1)
Title
:
DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE AND ALKALI METAL BINDING SITES
Authors
:
M. D. Toney, E. Hohenester, J. N. Jansonius
Date
:
12 Jul 94 (Deposition) - 15 Oct 94 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Biol. Unit 2: A (4x)
Keywords
:
Lyase(Decarboxylase)
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
M. D. Toney, E. Hohenester, S. W. Cowan, J. N. Jansonius
Dialkylglycine Decarboxylase Structure: Bifunctional Active Site And Alkali Metal Sites.
Science V. 261 756 1993
(for further references see the
PDB file header
)
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
3a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
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No.
Name
Count
Type
Full Name
1
MES
4
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2
NA
-1
Ligand/Ion
SODIUM ION
3
PLP
4
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: ME1 (UNKNOWN)
6: ME2 (UNKNOWN)
7: PLP (UNKNOWN)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:95 , THR A:98 , PRO A:99 , LEU A:102 , HOH A:526
BINDING SITE FOR RESIDUE NA A 435
2
AC2
SOFTWARE
LEU A:78 , VAL A:305 , ASP A:307 , HOH A:509 , HOH A:519
BINDING SITE FOR RESIDUE NA A 436
3
AC3
SOFTWARE
THR A:110 , GLY A:111 , ALA A:112 , ASN A:115 , TRP A:138 , HIS A:139 , GLU A:210 , ASP A:243 , ALA A:245 , GLN A:246 , LYS A:272 , THR A:302 , THR A:303 , MES A:434 , HOH A:536 , HOH A:544 , HOH A:552 , HOH A:621 , HOH A:625
BINDING SITE FOR RESIDUE PLP A 437
4
AC4
SOFTWARE
GLN A:52 , TRP A:138 , SER A:215 , GLN A:246 , LYS A:272 , ARG A:406 , PLP A:437 , HOH A:642
BINDING SITE FOR RESIDUE MES A 434
5
ME1
UNKNOWN
ALA A:95 , THR A:98 , PRO A:99 , LEU A:102
METAL BINDING SITE 1
6
ME2
UNKNOWN
LEU A:78 , VAL A:305 , ASP A:307
METAL BINDING SITE 2
7
PLP
UNKNOWN
LYS A:272 , PLP A:437
RESIDUE LYS 272 HAS THE COFACTOR PYRIDOXAL-5'- PHOSPHATE COVALENTLY ATTACHED TO IT
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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
(1, 4)
Info
All PROSITE Patterns/Profiles
1: AA_TRANSFER_CLASS_3 (A:240-277)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AA_TRANSFER_CLASS_3
PS00600
Aminotransferases class-III pyridoxal-phosphate attachment site.
DGDA_BURCE
240-277
4
A:240-277
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Exons
(0, 0)
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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
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2dkba_ (A:)
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Protein Domains
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)
(
)
Organisms
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)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PLP-dependent transferase-like
(627)
Superfamily
:
PLP-dependent transferases
(625)
Family
:
GABA-aminotransferase-like
(167)
Protein domain
:
Dialkylglycine decarboxylase
(13)
Pseudomonas cepacia [TaxId: 292]
(13)
1a
d2dkba_
A:
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2dkbA02 (A:61-324)
2a: CATH_2dkbA01 (A:29-60,A:325-433)
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Organisms
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)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Aspartate Aminotransferase; domain 2
(384)
Homologous Superfamily
:
Type I PLP-dependent aspartate aminotransferase-like (Major domain)
(384)
Burkholderia cepacia. Organism_taxid: 292.
(12)
1a
2dkbA02
A:61-324
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Aspartate Aminotransferase, domain 1
(355)
Homologous Superfamily
:
Aspartate Aminotransferase, domain 1
(354)
Burkholderia cepacia. Organism_taxid: 292.
(12)
2a
2dkbA01
A:29-60,A:325-433
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Pfam Domains
(0, 0)
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Asym.Unit (79 KB)
Header - Asym.Unit
Biol.Unit 1 (142 KB)
Header - Biol.Unit 1
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