EzCatDB: S00413
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DB codeS00413
RLCP classification3.113.90000.331 : Transfer
3.1143.50000.64 : Transfer
CATH domainDomain 13.30.930.10 : BirA Bifunctional Protein; domain 2Catalytic domain
E.C.6.3.1.1
CSA12as
MACiEM0075

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

Enzyme Name
UniProtKBKEGG

P00963
Protein nameAspartate--ammonia ligaseaspartate---ammonia ligase
asparagine synthetase
L-asparagine synthetase
SynonymsEC 6.3.1.1
Asparagine synthetase A
RefSeqNP_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)
PfamPF03590 (AsnA)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00252Alanine and aspartate metabolism
MAP00460Cyanoamino acid metabolism
MAP00910Nitrogen metabolism

UniProtKB:Accession NumberP00963
Entry nameASNA_ECOLI
ActivityATP + L-aspartate + NH(3) = AMP + diphosphate + L-asparagine.
SubunitHomodimer.
Subcellular locationCytoplasm.
Cofactor

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00002C00049C00014C00020C00013C00152
CompoundMagnesiumATPL-AspartateNH3AMPPyrophosphateL-Asparagine
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotideamino acids,carboxyl groupamine group,organic ionamine group,nucleotidephosphate group/phosphate ionamino acids,amide group
ChEBI18420
15422
17053
16134
16027
29888
17196
58048
PubChem888
5957
5960
44367445
222
6083
21961011
1023
6992089
6267
               
11asAUnboundUnboundUnboundUnboundUnboundUnboundBound:ASN
11asBUnboundUnboundUnboundUnboundUnboundUnboundBound:ASN
12asAUnboundUnboundUnboundUnboundBound:AMPUnboundBound:ASN
12asBUnboundUnboundUnboundUnboundBound:AMPUnboundBound:ASN

Active-site residues
resource
literature [5] & [6]
pdbCatalytic residuesCofactor-binding residuescomment
           
11asAASP 46;ARG 100;GLN 116
ASP 235;GLU 248(magnesium binding)
mutant C51A, C315A
11asBASP 46;ARG 100;GLN 116
ASP 235;GLU 248(magnesium binding)
mutant C51A, C315A
12asAASP 46;ARG 100;GLN 116
ASP 235;GLU 248(magnesium binding)
mutant C51A, C315A
12asBASP 46;ARG 100;GLN 116
ASP 235;GLU 248(magnesium binding)
mutant C51A, C315A

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[5]p.16
[6]Scheme 1, p.58003

references
[1]
PubMed ID22754
JournalJ Med Chem
Year1978
Volume21
Pages45-9
AuthorsBrynes S, Burckart GJ, Mokotoff M
TitlePotential inhibitors of L-asparagine biosynthesis. 4. Substituted sulfonamide and sulfonylhydrazide analogues of L-asparagine.
[2]
PubMed ID2858178
JournalArch Biochem Biophys
Year1985
Volume237
Pages335-46
AuthorsLuehr CA, Schuster SM
TitlePurification and characterization of beef pancreatic asparagine synthetase.
[3]
PubMed ID1346128
JournalJ Biol Chem
Year1992
Volume267
Pages144-9
AuthorsHinchman SK, Henikoff S, Schuster SM
TitleA relationship between asparagine synthetase A and aspartyl tRNA synthetase.
[4]
PubMed ID9559053
JournalAdv Enzymol Relat Areas Mol Biol
Year1998
Volume72
Pages145-98
AuthorsRichards NG, Schuster SM
TitleMechanistic issues in asparagine synthetase catalysis.
[5]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS)
Medline ID98100076
PubMed ID9437423
JournalNat Struct Biol
Year1998
Volume5
Pages15-9
AuthorsNakatsu T, Kato H, Oda J
TitleCrystal structure of asparagine synthetase reveals a close evolutionary relationship to class II aminoacyl-tRNA synthetase.
Related PDB11as,12as
Related UniProtKBP00963
[6]
JournalJ Am Chem Soc
Year1999
Volume121
Pages5799-800
AuthorsKoizumi M, Hiratake J, Nakatsu T, Kato H, Oda J,
TitleA Potent Transition-State Analogue Inhibitor of Escherichia coli Asparagine Synthetase A
[7]
PubMed ID10948265
JournalPlant Cell
Year2000
Volume12
Pages1491-509
AuthorsWang R, Guegler K, LaBrie ST, Crawford NM
TitleGenomic analysis of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate.

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).

createdupdated
2004-08-012009-02-26


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