D00300
type: Enzyme
rlcp: p56
cath: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
cath: Rossmann fold
ec: https://purl.uniprot.org/enzyme/6.3.5.4
csa: 1ct9
macie: M0302
uniprot: P22106
kegg enzyme: asparagine synthase (glutamine-hydrolysing)
kegg enzyme: asparagine synthetase (glutamine-hydrolysing)
kegg enzyme: glutamine-dependent asparagine synthetase
kegg enzyme: asparagine synthetase B
kegg enzyme: AS
kegg enzyme: AS-B
kegg pathway: Alanine and aspartate metabolism
kegg pathway: Nitrogen metabolism
kegg cofactor: Magnesium
kegg substrate: ATP
kegg substrate: L-Aspartate
kegg substrate: L-Glutamine
kegg substrate: H2O
kegg product: AMP
kegg product: Pyrophosphate
kegg product: L-Asparagine
kegg product: L-Glutamate
pdb: 1ct9A01
pdb: 1ct9B01
pdb: 1ct9C01
pdb: 1ct9D01
pdb: 1ct9A02
pdb: 1ct9B02
pdb: 1ct9C02
pdb: 1ct9D02
pdb bound state: Unbound
  compound: ATP
  pdb: 1ct9A01
pdb bound state: Unbound
  compound: ATP
  pdb: 1ct9B01
pdb bound state: Unbound
  compound: ATP
  pdb: 1ct9C01
pdb bound state: Unbound
  compound: ATP
  pdb: 1ct9D01
pdb bound state: Unbound
  compound: ATP
  pdb: 1ct9A02
pdb bound state: Unbound
  compound: ATP
  pdb: 1ct9B02
pdb bound state: Unbound
  compound: ATP
  pdb: 1ct9C02
pdb bound state: Unbound
  compound: ATP
  pdb: 1ct9D02
pdb bound state: Unbound
  compound: L-Aspartate
  pdb: 1ct9A01
pdb bound state: Unbound
  compound: L-Aspartate
  pdb: 1ct9B01
pdb bound state: Unbound
  compound: L-Aspartate
  pdb: 1ct9C01
pdb bound state: Unbound
  compound: L-Aspartate
  pdb: 1ct9D01
pdb bound state: Unbound
  compound: L-Aspartate
  pdb: 1ct9A02
pdb bound state: Unbound
  compound: L-Aspartate
  pdb: 1ct9B02
pdb bound state: Unbound
  compound: L-Aspartate
  pdb: 1ct9C02
pdb bound state: Unbound
  compound: L-Aspartate
  pdb: 1ct9D02
pdb bound state: Unbound
  compound: L-Glutamine
  pdb: 1ct9A02
pdb bound state: Unbound
  compound: L-Glutamine
  pdb: 1ct9B02
pdb bound state: Unbound
  compound: L-Glutamine
  pdb: 1ct9C02
pdb bound state: Unbound
  compound: L-Glutamine
  pdb: 1ct9D02
pdb bound state: Unbound
  compound: Magnesium
  pdb: 1ct9A01
pdb bound state: Unbound
  compound: Magnesium
  pdb: 1ct9B01
pdb bound state: Unbound
  compound: Magnesium
  pdb: 1ct9C01
pdb bound state: Unbound
  compound: Magnesium
  pdb: 1ct9D01
pdb bound state: Analogue
  compound: Magnesium
  pdb: 1ct9A02
  ligand het code: IUM_1102, IUM_1101
pdb bound state: Analogue
  compound: Magnesium
  pdb: 1ct9B02
  ligand het code: IUM_1109, IUM_1108
pdb bound state: Analogue
  compound: Magnesium
  pdb: 1ct9C02
  ligand het code: IUM_1116, IUM_1115
pdb bound state: Analogue
  compound: Magnesium
  pdb: 1ct9D02
  ligand het code: IUM_1123, IUM_1122
pdb bound state: Unbound
  compound: AMP
  pdb: 1ct9A01
pdb bound state: Unbound
  compound: AMP
  pdb: 1ct9B01
pdb bound state: Unbound
  compound: AMP
  pdb: 1ct9C01
pdb bound state: Unbound
  compound: AMP
  pdb: 1ct9D01
active site residues resources: Mapping the aspartic acid binding site of Escherichia coli asparagine synthetase B using substrate analogs.
active site residues resources: Crystal structure of asparagine synthetase reveals a close evolutionary relationship to class II aminoacyl-tRNA synthetase.
active site residues resources: Characterization of inhibitors acting at the synthetase site of Escherichia coli asparagine synthetase B.
references: Glutamine-dependent asparagine synthetase from leukemia cells. Chloride dependence, mechanism of action, and inhibition.
references: Glutamine-dependent nitrogen transfer in Escherichia coli asparagine synthetase B. Searching for the catalytic triad.
references: Arginine 30 and asparagine 74 have functional roles in the glutamine dependent activities of Escherichia coli asparagine synthetase B.
references: Mapping the aspartic acid binding site of Escherichia coli asparagine synthetase B using substrate analogs.
references: http://ezcatdb.cbrc.jp/EzCatDB/reference/D00300#5
references: Mutagenesis and chemical rescue indicate residues involved in beta-aspartyl-AMP formation by Escherichia coli asparagine synthetase B.
references: Crystal structure of asparagine synthetase reveals a close evolutionary relationship to class II aminoacyl-tRNA synthetase.
references: Kinetic mechanism of Escherichia coli asparagine synthetase B.
references: Three-dimensional structure of Escherichia coli asparagine synthetase B: a short journey from substrate to product.
references: Characterization of inhibitors acting at the synthetase site of Escherichia coli asparagine synthetase B.
references: Revisiting the steady state kinetic mechanism of glutamine-dependent asparagine synthetase from Escherichia coli.
comment: This enzyme is composed of two domains, N-terminal glutaminase domain, and C-terminal ligase domain. These domains catalyzes the following reactions: (A) Hydrolysis of glutamine amide (by the N-terminal glutaminase domain) (see [9]): (A#) This domain is homologous to the N-terminal glutaminase domain of Glutamine-fructose-6-phosphate transaminase (T00201 in EzCatDB), and has a similar reaction mechanism to its mechanism. (A1) Nucleophile, Cys1 can be either in an active conformation with the thiol group close to the substrate amide, or in an inactive one with the group pointing away from the substrate. During the catalysis, its conformation must be active. (A2) The N-terminal alpha-amino group acts as a general base, which activates the thiol group of the N-terminal Cys1, through a water molecule. (A3) The activated thiol group attacks the amide carbon of a substrate, glutamine, to form a tetrahedral intermediate. The intermediate is stabilized by an oxyanion hole, made up by mainchain amide groups of Asn74 and Gly75. (A4) The intermediate collapses to form a gamma-glutamylthioester and to release ammonia which might be protonated by the water bound to the alpha-amino group of Cys1. (A5) Another water (distinct from the above bound water) is activated through the bound water by the alpha-amino group. (A6) The activated water makes a nucleophilic attack on the thiolester carbon, to form a tetrahedral intermediate. This intermediate is also stabilized by the oxyanion hole. (A7) The intermediate collapses to release the product, glutamate, from Cys1, and the thiol group is protonated through the bound water. (B) Transfer of adenylate (AMP) to carboxylate oxygen of Aspartate: (C) Transfer of acyl group of Asp-AMP intermediate to ammonia:

Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.60.20.10
catalytic domain: index.html

Rossmann fold
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.40.50.620
catalytic domain: index.html

Alanine and aspartate metabolism
type: KeggPathway
references: KEGG:MAP00252

Nitrogen metabolism
type: KeggPathway
references: KEGG:MAP00910

Magnesium
type: KeggCofactor
references: KEGG:C00305
compound type: divalent metal (Ca2+, Mg2+)
references: CHEBI:18420
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

ATP
type: KeggSubstrate
references: KEGG:C00002
compound type: amine group
compound type: nucleotide
references: CHEBI:15422
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

L-Aspartate
type: KeggSubstrate
references: KEGG:C00049
compound type: amino acids
compound type: carboxyl group
references: CHEBI:17053
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

L-Glutamine
type: KeggSubstrate
references: KEGG:C00064
compound type: amino acids
compound type: amide group
references: CHEBI:18050
references: CHEBI:58359
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

H2O
type: KeggSubstrate
references: KEGG:C00001
compound type: H2O
references: CHEBI:15377
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

AMP
type: KeggProduct
references: KEGG:C00020
compound type: amine group
compound type: nucleotide
references: CHEBI:16027
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Pyrophosphate
type: KeggProduct
references: KEGG:C00013
compound type: phosphate group/phosphate ion
references: CHEBI:29888
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

L-Asparagine
type: KeggProduct
references: KEGG:C00152
compound type: amino acids
compound type: amide group
references: CHEBI:17196
references: CHEBI:58048
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

L-Glutamate
type: KeggProduct
references: KEGG:C00025
compound type: amino acids
compound type: carboxyl group
references: CHEBI:16015
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

1ct9A01
type: Pdb
references: 1ct9
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ct9
catalytic residue: ;ASN 74
main chain in catalysis: GLY 75
comment: mutant C1A

1ct9B01
type: Pdb
references: 1ct9
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ct9
catalytic residue: ;ASN 74
main chain in catalysis: GLY 75
comment: mutant C1A

1ct9C01
type: Pdb
references: 1ct9
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ct9
catalytic residue: ;ASN 74
main chain in catalysis: GLY 75
comment: mutant C1A

1ct9D01
type: Pdb
references: 1ct9
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ct9
catalytic residue: ;ASN 74
main chain in catalysis: GLY 75
comment: mutant C1A

1ct9A02
type: Pdb
references: 1ct9
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ct9
catalytic residue: ARG 324
cofactor binding residue: GLU 352;TYR 357;ASP 384(Magnesium-1 binding);ASP 238;ASP 351(Magnesium-2 binding)

1ct9B02
type: Pdb
references: 1ct9
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ct9
catalytic residue: ARG 324
cofactor binding residue: GLU 352;TYR 357;ASP 384(Magnesium-1 binding);ASP 238;ASP 351(Magnesium-2 binding)

1ct9C02
type: Pdb
references: 1ct9
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ct9
catalytic residue: ARG 324
cofactor binding residue: GLU 352;TYR 357;ASP 384(Magnesium-1 binding);ASP 238;ASP 351(Magnesium-2 binding)

1ct9D02
type: Pdb
references: 1ct9
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ct9
catalytic residue: ARG 324
cofactor binding residue: GLU 352;TYR 357;ASP 384(Magnesium-1 binding);ASP 238;ASP 351(Magnesium-2 binding)

Glutamine-dependent asparagine synthetase from leukemia cells. Chloride dependence, mechanism of action, and inhibition.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/5076775
journal: J Biol Chem
volume: 247
pages: 6708-19
published year: 1972
authors:
  item: Horowitz B
  item: Meister A

Glutamine-dependent nitrogen transfer in Escherichia coli asparagine synthetase B. Searching for the catalytic triad.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7907328
journal: J Biol Chem
volume: 269
pages: 7450-7
published year: 1994
authors:
  item: Boehlein SK
  item: Richards NG
  item: Schuster SM

Arginine 30 and asparagine 74 have functional roles in the glutamine dependent activities of Escherichia coli asparagine synthetase B.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7929415
journal: J Biol Chem
volume: 269
pages: 26789-95
published year: 1994
authors:
  item: Boehlein SK
  item: Richards NG
  item: Walworth ES
  item: Schuster SM

Mapping the aspartic acid binding site of Escherichia coli asparagine synthetase B using substrate analogs.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8691431
journal: J Med Chem
volume: 39
pages: 2367-78
published year: 1996
authors:
  item: Parr IB
  item: Boehlein SK
  item: Dribben AB
  item: Schuster SM
  item: Richards NG

http://ezcatdb.cbrc.jp/EzCatDB/reference/D00300#5
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 1-240
references: http://www.ncbi.nlm.nih.gov/pubmed/8805567
journal: Structure
volume: 4
pages: 801-10
published year: 1996
authors:
  item: Isupov MN
  item: Obmolova G
  item: Butterworth S
  item: Badet-Denisot MA
  item: Badet B
  item: Polikarpov I
  item: Littlechild JA
  item: Teplyakov A
title: Substrate binding is required for assembly of the active conformation of the catalytic site in Ntn amidotransferases: evidence from the 1.8 A crystal structure of the glutaminase domain of glucosamine 6-phosphate synthase.

Mutagenesis and chemical rescue indicate residues involved in beta-aspartyl-AMP formation by Escherichia coli asparagine synthetase B.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9139684
journal: J Biol Chem
volume: 272
pages: 12384-92
published year: 1997
authors:
  item: Boehlein SK
  item: Walworth ES
  item: Richards NG
  item: Schuster SM

Crystal structure of asparagine synthetase reveals a close evolutionary relationship to class II aminoacyl-tRNA synthetase.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9437423
journal: Nat Struct Biol
volume: 5
pages: 15-9
published year: 1998
authors:
  item: Nakatsu T
  item: Kato H
  item: Oda J

Kinetic mechanism of Escherichia coli asparagine synthetase B.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9748330
journal: Biochemistry
volume: 37
pages: 13230-8
published year: 1998
authors:
  item: Boehlein SK
  item: Stewart JD
  item: Walworth ES
  item: Thirumoorthy R
  item: Richards NG
  item: Schuster SM

Three-dimensional structure of Escherichia coli asparagine synthetase B: a short journey from substrate to product.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS)
medline id: 20056034
references: http://www.ncbi.nlm.nih.gov/pubmed/10587437
journal: Biochemistry
volume: 38
pages: 16146-57
published year: 1999
authors:
  item: Larsen TM
  item: Boehlein SK
  item: Schuster SM
  item: Richards NG
  item: Thoden JB
  item: Holden HM
  item: Rayment I
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P22106

Characterization of inhibitors acting at the synthetase site of Escherichia coli asparagine synthetase B.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11551215
journal: Biochemistry
volume: 40
pages: 11168-75
published year: 2001
authors:
  item: Boehlein SK
  item: Nakatsu T
  item: Hiratake J
  item: Thirumoorthy R
  item: Stewart JD
  item: Richards NG
  item: Schuster SM

Revisiting the steady state kinetic mechanism of glutamine-dependent asparagine synthetase from Escherichia coli.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12706338
journal: Arch Biochem Biophys
volume: 413
pages: 23-31
published year: 2003
authors:
  item: Tesson AR
  item: Soper TS
  item: Ciustea M
  item: Richards NG

ReferenceForCatalyticMechanism
reference index: 2
reference section: Fig.1
reference step: 5

ReferenceForCatalyticMechanism
reference index: 3
reference section: Fig.3, Fig.4

ReferenceForCatalyticMechanism
reference index: 5
reference section: Fig.6, p.807
reference step: 6

ReferenceForCatalyticMechanism
reference index: 6
reference section: Fig.4

ReferenceForCatalyticMechanism
reference index: 9
reference section: p.16151