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1TUF
Biol. Unit 2
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Asym.Unit (149 KB)
Biol.Unit 1 (145 KB)
Biol.Unit 2 (285 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIAMINOPIMELATE DECARBOXYLASE FROM M. JANNASCHI
Authors
:
K. Rajashankar, S. R. Ray, J. B. Bonanno, M. G. Pinho, G. He, H. De Lencastre, A. Tomasz, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date
:
24 Jun 04 (Deposition) - 20 Jul 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (2x)
Keywords
:
Antibiotic Resistance, Diamnopimilate Decarboxylase, Lysine Biosynthesis, Structural Genomics, Nysgxrc, T135, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Rajashankar, S. R. Ray, J. B. Bonanno, M. G. Pinho, G. He, H. De Lencastre, A. Tomasz, S. K. Burley
Cocrystal Structures Of Diaminopimelate Decarboxylase: Mechanism, Evolution, And Inhibition Of An Antibiotic Resistance Accessory Factor
Structure V. 10 1499 2002
(for further references see the
PDB file header
)
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: AZELAIC ACID (AZ1a)
1b: AZELAIC ACID (AZ1b)
2a: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPa)
2b: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
AZ1
4
Ligand/Ion
AZELAIC ACID
2
LLP
4
Mod. Amino Acid
2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LLP A:83 , HIS A:224 , GLY A:226 , SER A:227 , ARG A:307 , ARG A:343 , TYR A:347 , HOH A:532 , GLU B:373 , SER B:374 , TYR B:409
BINDING SITE FOR RESIDUE AZ1 A 502
2
AC2
SOFTWARE
CYS A:372 , GLU A:373 , SER B:227 , ARG B:307 , ARG B:343 , TYR B:347
BINDING SITE FOR RESIDUE AZ1 B 503
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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
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ODR_DC_2_1 (A:80-98,B:80-98)
2: ODR_DC_2_2 (A:253-266,B:253-266)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ODR_DC_2_1
PS00878
Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.
DCDA_METJA
70-88
4
A:80-98
B:80-98
2
ODR_DC_2_2
PS00879
Orn/DAP/Arg decarboxylases family 2 signature 2.
DCDA_METJA
243-256
4
A:253-266
B:253-266
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1tufa1 (A:15-49,A:314-448)
1b: SCOP_d1tufb1 (B:15-49,B:314-448)
2a: SCOP_d1tufa2 (A:50-313)
2b: SCOP_d1tufb2 (B:50-313)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Domain of alpha and beta subunits of F1 ATP synthase-like
(89)
Superfamily
:
Alanine racemase C-terminal domain-like
(25)
Family
:
Eukaryotic ODC-like
(13)
Protein domain
:
Diaminopimelate decarboxylase LysA
(6)
Methanococcus jannaschii [TaxId: 2190]
(2)
1a
d1tufa1
A:15-49,A:314-448
1b
d1tufb1
B:15-49,B:314-448
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
PLP-binding barrel
(27)
Family
:
Alanine racemase-like, N-terminal domain
(25)
Protein domain
:
Diaminopimelate decarboxylase LysA
(6)
Methanococcus jannaschii [TaxId: 2190]
(2)
2a
d1tufa2
A:50-313
2b
d1tufb2
B:50-313
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1tufA02 (A:51-306)
1b: CATH_1tufB02 (B:51-306)
2a: CATH_1tufA01 (A:15-50,A:307-448)
2b: CATH_1tufB01 (B:15-50,B:307-448)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Alanine racemase
(53)
Methanocaldococcus jannaschii. Organism_taxid: 2190.
(2)
1a
1tufA02
A:51-306
1b
1tufB02
B:51-306
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Lyase, Ornithine Decarboxylase; Chain A, domain 1
(47)
Homologous Superfamily
:
Lyase, Ornithine Decarboxylase; Chain A, domain 1
(47)
Methanocaldococcus jannaschii. Organism_taxid: 2190.
(2)
2a
1tufA01
A:15-50,A:307-448
2b
1tufB01
B:15-50,B:307-448
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Orn_Arg_deC_N_1tufB01 (B:58-312)
1b: PFAM_Orn_Arg_deC_N_1tufB02 (B:58-312)
2a: PFAM_Orn_DAP_Arg_deC_1tufB03 (B:236-420)
2b: PFAM_Orn_DAP_Arg_deC_1tufB04 (B:236-420)
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Clan
:
TIM_barrel
(694)
Family
:
Orn_Arg_deC_N
(17)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth
(2)
1a
Orn_Arg_deC_N-1tufB01
B:58-312
1b
Orn_Arg_deC_N-1tufB02
B:58-312
Clan
:
no clan defined [family: Orn_DAP_Arg_deC]
(18)
Family
:
Orn_DAP_Arg_deC
(18)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth
(2)
2a
Orn_DAP_Arg_deC-1tufB03
B:236-420
2b
Orn_DAP_Arg_deC-1tufB04
B:236-420
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Asym.Unit (149 KB)
Header - Asym.Unit
Biol.Unit 1 (145 KB)
Header - Biol.Unit 1
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Header - Biol.Unit 2
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