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1TWI
Biol. Unit 2
Info
Asym.Unit (309 KB)
Biol.Unit 1 (153 KB)
Biol.Unit 2 (157 KB)
Biol.Unit 3 (304 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIAMINOPIMELATE DECARBOXYLASE FROM M. JANNASCHII IN CO-COMPLEX WITH L-LYSINE
Authors
:
K. R. Rajashankar, S. S. Ray, J. B. Bonanno, M. G. Pinho, G. He, H. De Lenc A. Tomasz, S. K. Burley, New York Sgx Research Center For Struct Genomics (Nysgxrc)
Date
:
01 Jul 04 (Deposition) - 27 Jul 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Antibiotic Resistance, Diaminopimelate 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. R. Rajashankar, S. S. 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
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: LYSINE (LYSa)
1b: LYSINE (LYSb)
1c: LYSINE (LYSc)
1d: LYSINE (LYSd)
1e: LYSINE (LYSe)
1f: LYSINE (LYSf)
2a: MAGNESIUM ION (MGa)
3a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
3b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
3c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
3d: PYRIDOXAL-5'-PHOSPHATE (PLPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
LYS
6
Mod. Amino Acid
LYSINE
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
[
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Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH C:1688 , HOH C:1711 , HOH C:1728 , HOH C:1729 , HOH C:1842
BINDING SITE FOR RESIDUE MG C 1607
02
AC2
SOFTWARE
SER A:227 , ARG A:307 , ARG A:343 , TYR A:347 , TYR A:401 , PLP A:1501 , GLU B:373 , TYR B:409 , HOH D:1764 , HOH D:1876 , HOH D:1937
BINDING SITE FOR RESIDUE LYS D 1601
03
AC3
SOFTWARE
CYS A:372 , GLU A:373 , TYR A:409 , ARG B:307 , ARG B:343 , TYR B:347 , TYR B:401 , MET B:405 , PLP B:1502 , HOH B:1782 , HOH D:1815
BINDING SITE FOR RESIDUE LYS D 1602
04
AC4
SOFTWARE
SER C:227 , ARG C:307 , ARG C:343 , TYR C:347 , TYR C:401 , MET C:405 , PLP C:1503 , CYS D:372 , GLU D:373 , TYR D:409
BINDING SITE FOR RESIDUE LYS D 1603
05
AC5
SOFTWARE
ARG C:172 , ASN C:192 , PHE C:194 , HIS C:224 , ILE C:225 , SER C:227 , HOH D:1966 , HOH D:1984
BINDING SITE FOR RESIDUE LYS D 1604
06
AC6
SOFTWARE
GLU C:373 , TYR C:409 , SER D:227 , ARG D:307 , ARG D:343 , TYR D:347 , TYR D:401 , MET D:405 , PLP D:1504 , LYS D:1606 , HOH D:1850
BINDING SITE FOR RESIDUE LYS D 1605
07
AC7
SOFTWARE
SER C:374 , ARG D:172 , ASN D:192 , PHE D:194 , HIS D:224 , ILE D:225 , GLY D:226 , SER D:227 , LYS D:1605 , HOH D:1897 , HOH D:1955 , HOH D:1965
BINDING SITE FOR RESIDUE LYS D 1606
08
AC8
SOFTWARE
ALA A:81 , LYS A:83 , ASP A:102 , ASN A:125 , HIS A:224 , SER A:227 , GLY A:264 , GLU A:304 , GLY A:306 , ARG A:307 , TYR A:401 , HOH A:1505 , HOH A:1525 , HOH A:1538 , CYS B:372 , LYS D:1601
BINDING SITE FOR RESIDUE PLP A 1501
09
AC9
SOFTWARE
CYS A:372 , ALA B:81 , LYS B:83 , ASP B:102 , ASN B:125 , HIS B:224 , SER B:227 , GLY B:264 , GLU B:304 , GLY B:306 , ARG B:307 , TYR B:401 , HOH B:1512 , HOH B:1526 , HOH B:1553 , HOH B:1785 , LYS D:1602
BINDING SITE FOR RESIDUE PLP B 1502
10
BC1
SOFTWARE
ALA C:81 , LYS C:83 , ASP C:102 , HIS C:224 , SER C:227 , GLY C:264 , GLU C:304 , GLY C:306 , ARG C:307 , TYR C:401 , HOH C:1609 , HOH C:1630 , HOH C:1641 , HOH C:1716 , CYS D:372 , LYS D:1603
BINDING SITE FOR RESIDUE PLP C 1503
11
BC2
SOFTWARE
CYS C:372 , ALA D:81 , LYS D:83 , ASP D:102 , ASN D:125 , HIS D:224 , SER D:227 , GLY D:264 , GLU D:304 , GLY D:306 , ARG D:307 , TYR D:401 , LYS D:1605 , HOH D:1627 , HOH D:1632 , HOH D:1645 , HOH D:1731
BINDING SITE FOR RESIDUE PLP D 1504
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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, 4)
Info
All PROSITE Patterns/Profiles
1: ODR_DC_2_1 (C:80-98,D:80-98)
2: ODR_DC_2_2 (C:253-266,D:253-266)
;
View:
Select:
Label:
End label:
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
2
-
-
C:80-98
D:80-98
2
ODR_DC_2_2
PS00879
Orn/DAP/Arg decarboxylases family 2 signature 2.
DCDA_METJA
243-256
2
-
-
C:253-266
D:253-266
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1twia1 (A:15-49,A:314-448)
1b: SCOP_d1twib1 (B:15-49,B:314-448)
1c: SCOP_d1twic1 (C:15-49,C:314-448)
1d: SCOP_d1twid1 (D:15-49,D:314-448)
2a: SCOP_d1twia2 (A:50-313)
2b: SCOP_d1twib2 (B:50-313)
2c: SCOP_d1twic2 (C:50-313)
2d: SCOP_d1twid2 (D: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
d1twia1
A:15-49,A:314-448
1b
d1twib1
B:15-49,B:314-448
1c
d1twic1
C:15-49,C:314-448
1d
d1twid1
D:15-49,D: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
d1twia2
A:50-313
2b
d1twib2
B:50-313
2c
d1twic2
C:50-313
2d
d1twid2
D:50-313
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1twiA02 (A:51-306)
1b: CATH_1twiB02 (B:51-306)
1c: CATH_1twiC02 (C:51-306)
1d: CATH_1twiD02 (D:51-306)
2a: CATH_1twiA01 (A:15-50,A:307-448)
2b: CATH_1twiB01 (B:15-50,B:307-448)
2c: CATH_1twiC01 (C:15-50,C:307-448)
2d: CATH_1twiD01 (D:15-50,D:307-448)
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)
Homologous Superfamilies
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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
1twiA02
A:51-306
1b
1twiB02
B:51-306
1c
1twiC02
C:51-306
1d
1twiD02
D: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
1twiA01
A:15-50,A:307-448
2b
1twiB01
B:15-50,B:307-448
2c
1twiC01
C:15-50,C:307-448
2d
1twiD01
D:15-50,D:307-448
[
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Orn_Arg_deC_N_1twiD01 (D:58-312)
1b: PFAM_Orn_Arg_deC_N_1twiD02 (D:58-312)
1c: PFAM_Orn_Arg_deC_N_1twiD03 (D:58-312)
1d: PFAM_Orn_Arg_deC_N_1twiD04 (D:58-312)
2a: PFAM_Orn_DAP_Arg_deC_1twiD05 (D:236-420)
2b: PFAM_Orn_DAP_Arg_deC_1twiD06 (D:236-420)
2c: PFAM_Orn_DAP_Arg_deC_1twiD07 (D:236-420)
2d: PFAM_Orn_DAP_Arg_deC_1twiD08 (D:236-420)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
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-1twiD01
D:58-312
1b
Orn_Arg_deC_N-1twiD02
D:58-312
1c
Orn_Arg_deC_N-1twiD03
D:58-312
1d
Orn_Arg_deC_N-1twiD04
D: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-1twiD05
D:236-420
2b
Orn_DAP_Arg_deC-1twiD06
D:236-420
2c
Orn_DAP_Arg_deC-1twiD07
D:236-420
2d
Orn_DAP_Arg_deC-1twiD08
D:236-420
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