DB code: S00413

RLCP classification 3.113.90000.331 : Transfer
3.1143.50000.64 : Transfer
CATH domain 3.30.930.10 : BirA Bifunctional Protein; domain 2 Catalytic domain
E.C. 6.3.1.1
CSA 12as
M-CSA 12as
MACiE M0075

CATH domain Related DB codes (homologues)
3.30.930.10 : BirA Bifunctional Protein; domain 2 D00291 D00293 D00294 D00295 M00049 T00113

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P00963 Aspartate--ammonia ligase
EC 6.3.1.1
Asparagine synthetase A
NP_418200.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_006952153.1 (Protein)
NC_019049.1 (DNA/RNA sequence)
YP_491685.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF03590 (AsnA)
[Graphical View]

KEGG enzyme name
aspartate---ammonia ligase
asparagine synthetase
L-asparagine synthetase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P00963 ASNA_ECOLI ATP + L-aspartate + NH(3) = AMP + diphosphate + L-asparagine. Homodimer. Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00252 Alanine and aspartate metabolism
MAP00460 Cyanoamino acid metabolism
MAP00910 Nitrogen metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C00049 C00014 C00020 C00013 C00152
E.C.
Compound Magnesium ATP L-Aspartate NH3 AMP Pyrophosphate L-Asparagine
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide amino acids,carboxyl group amine group,organic ion amine group,nucleotide phosphate group/phosphate ion amino acids,amide group
ChEBI 18420
15422
17053
16134
16027
29888
17196
58048
PubChem 888
5957
44367445
5960
222
6083
1023
21961011
6267
6992089
11asA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Bound:ASN
11asB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Bound:ASN
12asA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:AMP Unbound Bound:ASN
12asB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:AMP Unbound Bound:ASN

Reference for Active-site residues
resource references E.C.
literature [5] & [6]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
11asA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 46;ARG 100;GLN 116 ASP 235;GLU 248(magnesium binding) mutant C51A, C315A
11asB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 46;ARG 100;GLN 116 ASP 235;GLU 248(magnesium binding) mutant C51A, C315A
12asA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 46;ARG 100;GLN 116 ASP 235;GLU 248(magnesium binding) mutant C51A, C315A
12asB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 46;ARG 100;GLN 116 ASP 235;GLU 248(magnesium binding) mutant C51A, C315A

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[5]
p.16
[6]
Scheme 1, p.5800 3

References
[1]
Resource
Comments
Medline ID
PubMed ID 22754
Journal J Med Chem
Year 1978
Volume 21
Pages 45-9
Authors Brynes S, Burckart GJ, Mokotoff M
Title Potential inhibitors of L-asparagine biosynthesis. 4. Substituted sulfonamide and sulfonylhydrazide analogues of L-asparagine.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2858178
Journal Arch Biochem Biophys
Year 1985
Volume 237
Pages 335-46
Authors Luehr CA, Schuster SM
Title Purification and characterization of beef pancreatic asparagine synthetase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 1346128
Journal J Biol Chem
Year 1992
Volume 267
Pages 144-9
Authors Hinchman SK, Henikoff S, Schuster SM
Title A relationship between asparagine synthetase A and aspartyl tRNA synthetase.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 9559053
Journal Adv Enzymol Relat Areas Mol Biol
Year 1998
Volume 72
Pages 145-98
Authors Richards NG, Schuster SM
Title Mechanistic issues in asparagine synthetase catalysis.
Related PDB
Related UniProtKB
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS)
Medline ID 98100076
PubMed ID 9437423
Journal Nat Struct Biol
Year 1998
Volume 5
Pages 15-9
Authors Nakatsu T, Kato H, Oda J
Title Crystal structure of asparagine synthetase reveals a close evolutionary relationship to class II aminoacyl-tRNA synthetase.
Related PDB 11as 12as
Related UniProtKB P00963
[6]
Resource
Comments
Medline ID
PubMed ID
Journal J Am Chem Soc
Year 1999
Volume 121
Pages 5799-800
Authors Koizumi M, Hiratake J, Nakatsu T, Kato H, Oda J,
Title A Potent Transition-State Analogue Inhibitor of Escherichia coli Asparagine Synthetase A
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 10948265
Journal Plant Cell
Year 2000
Volume 12
Pages 1491-509
Authors Wang R, Guegler K, LaBrie ST, Crawford NM
Title Genomic analysis of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate.
Related PDB
Related UniProtKB

Comments
Asparagine synthase A (S00413) catalyzes NH3-dependent activity, whilst asparagine synthase B (E.C. 6.3.5.4; D00300) catalyzes glutamine-dependent activity.
According to the literature [5] & [6], this enzyme catalyzes two successive transfer reactions. Firstly, this enzyme transfers adenylate from ATP to the beta-carboxylate of another substrate, L-aspartate forming an intermediate, beta-aspartyl adenylate. Secondly, it transfers acyl group of the intermediate to ammonia (NH3), releasing diphosphate.
The first reaction (adenylate transfer) proceeds as follows (see [5] & [6]):
(1) The acceptor group, the beta-carboxylate oxygen atom of the substrate, L-aspartate, makes a nucleophilic attack on the transferred group, the phosphorus atom of the alpha-phosphate group of ATP. At this step, Gln116 seems to stabilize the acceptor, the beta-carboxylate.
(2) Arg100 stabilizes the transferred group, the alpha-phosphate of ATP, whereas Arg299 and magnesium ion bound to Asp235 and Glu248 stabilize the leaving group, the beta- and gamma-phosphate groups of ATP.
(3) The leaving group, the diphosphate will be released.
The second reaction (acyl transfer) proceeds as follows (see [5] & [6]):
(1') The acceptor group, ammonia, makes a nucleophilic attack on the carbonyl carbon of the adenylated aspartate intermediate, forming a tetrahedral oxyanion transtion-state or intermediate, which has a zwitterionic character.
(2') Arg106 and Gln116 stabilize the negative charge on the oxyanion part of the transition-state or intermediate, whilst Asp46 stabilizes the positive charge on the -NH3(+) part.
(3') Asp46 acts as a general base, to deprotonate the -NH3 group of the transition-state/intermediate, releasing the leaving group, adenylate (AMP).

Created Updated
2004-08-01 2009-02-26