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1YNI
Biol. Unit 1
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Asym.Unit (295 KB)
Biol.Unit 1 (148 KB)
Biol.Unit 2 (146 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF N-SUCCINYLARGININE DIHYDROLASE, ASTB, BOUND TO SUBSTRATE AND PRODUCT, AN ENZYME FROM THE ARGININE CATABOLIC PATHWAY OF ESCHERICHIA COLI
Authors
:
A. Tocilj, J. D. Schrag, Y. Li, B. L. Schneider, L. Reitzer, A. Matte, M. Cygler, Montreal-Kingston Bacterial Structural Genomics Initiative (Bsgi)
Date
:
24 Jan 05 (Deposition) - 15 Feb 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,D (1x)
Biol. Unit 2: B,C (1x)
Keywords
:
Succinylarginine, Dihydrolase, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Structural Genomics
(Keyword Search:
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]
)
Reference
:
A. Tocilj, J. D. Schrag, Y. Li, B. L. Schneider, L. Reitzer, A. Matte, M. Cygler
Crystal Structure Of N-Succinylarginine Dihydrolase Astb, Bound To Substrate And Product, An Enzyme From The Arginine Catabolic Pathway Of Escherichia Coli.
J. Biol. Chem. V. 280 15800 2005
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
2a: N~2~-(3-CARBOXYPROPANOYL)-L-ARGINI... (SUGa)
2b: N~2~-(3-CARBOXYPROPANOYL)-L-ARGINI... (SUGb)
2c: N~2~-(3-CARBOXYPROPANOYL)-L-ARGINI... (SUGc)
2d: N~2~-(3-CARBOXYPROPANOYL)-L-ARGINI... (SUGd)
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No.
Name
Count
Type
Full Name
1
K
-1
Ligand/Ion
POTASSIUM ION
2
SUG
2
Ligand/Ion
N~2~-(3-CARBOXYPROPANOYL)-L-ARGININE
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Sites
(4, 4)
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1: AC1 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC8 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU A:338 , LEU A:339 , ALA A:341 , ASN A:343 , ILE A:345 , HOH A:2155
BINDING SITE FOR RESIDUE K A 2001
2
AC4
SOFTWARE
LEU D:338 , LEU D:339 , ALA D:341 , ASN D:343 , ILE D:345 , HOH D:2163
BINDING SITE FOR RESIDUE K D 2004
3
AC5
SOFTWARE
HIS A:17 , ALA A:19 , GLY A:20 , LEU A:21 , SER A:22 , ASN A:25 , SER A:28 , TRP A:107 , ALA A:109 , ASN A:110 , HIS A:137 , ARG A:138 , ALA A:177 , ARG A:212 , PHE A:247 , HIS A:248 , ASP A:250 , ASN A:359 , GLY A:360 , SER A:365 , HOH A:2128
BINDING SITE FOR RESIDUE SUG A 1001
4
AC8
SOFTWARE
HIS D:17 , ALA D:19 , GLY D:20 , LEU D:21 , SER D:22 , ASN D:25 , SER D:28 , TRP D:107 , ALA D:109 , ASN D:110 , HIS D:137 , ARG D:138 , ALA D:177 , ARG D:212 , PHE D:247 , HIS D:248 , ASP D:250 , ASN D:359 , GLY D:360 , SER D:365 , HOH D:2075
BINDING SITE FOR RESIDUE SUG D 1004
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SAPs(SNPs)/Variants
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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, 4)
Info
All SCOP Domains
1a: SCOP_d1ynib_ (B:)
1b: SCOP_d1ynic_ (C:)
1c: SCOP_d1ynid_ (D:)
2a: SCOP_d1ynia1 (A:2-441)
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Protein Domains
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Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Pentein, beta/alpha-propeller
(68)
Superfamily
:
Pentein
(68)
Family
:
Succinylarginine dihydrolase-like
(5)
Protein domain
:
automated matches
(3)
Escherichia coli [TaxId: 562]
(3)
1a
d1ynib_
B:
1b
d1ynic_
C:
1c
d1ynid_
D:
Protein domain
:
Succinylarginine dihydrolase
(2)
Escherichia coli [TaxId: 562]
(2)
2a
d1ynia1
A:2-441
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1yniA00 (A:2-441)
1b: CATH_1yniB00 (B:2-441)
1c: CATH_1yniC00 (C:2-441)
1d: CATH_1yniD00 (D:2-441)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
5-stranded Propeller
(36)
Topology
:
L-arginine/glycine Amidinotransferase; Chain A
(36)
Homologous Superfamily
:
n-succinylarginine dihydrolase, astb
(3)
Escherichia coli. Organism_taxid: 562.
(3)
1a
1yniA00
A:2-441
1b
1yniB00
B:2-441
1c
1yniC00
C:2-441
1d
1yniD00
D:2-441
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_AstB_1yniD01 (D:2-441)
1b: PFAM_AstB_1yniD02 (D:2-441)
1c: PFAM_AstB_1yniD03 (D:2-441)
1d: PFAM_AstB_1yniD04 (D:2-441)
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Clan
:
GME
(20)
Family
:
AstB
(2)
Escherichia coli (strain K12)
(2)
1a
AstB-1yniD01
D:2-441
1b
AstB-1yniD02
D:2-441
1c
AstB-1yniD03
D:2-441
1d
AstB-1yniD04
D:2-441
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Asymmetric Unit 1
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Asym.Unit (295 KB)
Header - Asym.Unit
Biol.Unit 1 (148 KB)
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