EzCatDB: T00109

DB codeT00109
RLCP classification3.113.90020.1181
3.1143.80000.1190
CATH domainDomain 13.40.50.720
Domain 23.40.1190.10Catalytic domain
Domain 33.90.190.20
E.C.6.3.2.9
CSA1uag
MACiEM0317

CATH domainRelated DB codes (homologues)
3.40.1190.10D00516
3.40.50.720S00543,S00551,S00552,S00553,S00602,S00604,S00605,S00608,S00610,S00625,S00319,S00328,S00329,S00330,S00331,S00332,D00456,D00457,D00458,S00324,S00320,S00325,S00326,S00327,D00459,S00335,S00336,S00334,T00219,S00339,D00513,D00001,D00002,D00003,D00005,D00007,D00008,D00010,D00012,D00017,D00018,D00023,D00027,D00028,D00031,D00032,D00033,D00034,D00035,D00037,D00048,D00071,D00476,D00481,D00482,D00490,D00492,D00494,D00545,D00601,D00603,D00604,D00605,D00615,D00845,D00857,D00858,M00161,M00171,M00210,T00002,T00010,T00011,T00015,T00227,T00247,T00408,T00414,D00827,D00262,D00274,D00275,M00035
3.90.190.20D00516

Enzyme Name
Swiss-protKEGG

P14900
Protein nameUDP-N-acetylmuramoylalanine--D-glutamate ligaseUDP-N-acetylmuramoyl-L-alanine---D-glutamate ligase
MurD synthetase
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase
uridine diphospho-N-acetylmuramoylalanyl-D-glutamate synthetase
D-glutamate-adding enzyme
D-glutamate ligase
UDP-Mur-NAC-L-Ala:D-Glu ligase
UDP-N-acetylmuramoyl-L-alanine:glutamate ligase (ADP-forming)
UDP-N-acetylmuramoylalanine---D-glutamate ligase
SynonymsEC 6.3.2.9
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase
D-glutamic acid-adding enzyme

KEGG pathways
MAP codePathways
MAP00471D-Glutamine and D-glutamate metabolism
MAP00550Peptidoglycan biosynthesis

Swiss-prot:Accession NumberP14900
Entry nameMURD_ECOLI
ActivityATP + UDP-N-acetylmuramoyl-L-alanine + glutamate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D- glutamate.
Subunit
Subcellular locationCytoplasm.
Cofactor


CofactorsSubstratesProducts
KEGG-idC00305C00002C01212C00302C00008C00009C00692
CompoundMagnesiumATPUDP-N-acetylmuramoyl-L-alanineGlutamateADPOrthophosphateUDP-N-acetylmuramoyl-L-alanyl-D-glutamate
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotideamino acids,amide group,carbohydrate,nucleotideamino acids,carboxyl groupamine group,nucleotidephosphate group/phosphate ionamino acids,amide group,carbohydrate,carboxyl group,nucleotide,peptide/protein
1e0dA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1eehA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1uagA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
2uagA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
3uagA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
4uagA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1e0dA02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1eehA03UnboundUnboundBound:UMAUnboundUnboundUnboundUnbound
1uagA02UnboundUnboundBound:UMAUnboundUnboundAnalogue:SO4Unbound
2uagA02Bound:2x_MGUnboundBound:UMAUnboundBound:ADPUnboundUnbound
3uagA02Analogue:_MNUnboundBound:UMAUnboundBound:ADPUnboundUnbound
4uagA02UnboundUnboundUnboundUnboundUnboundAnalogue:SO4Bound:UAG
1e0dA03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1eehA02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1uagA03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
2uagA03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
3uagA03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
4uagA03UnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
PDB;2uag & literature [3]
pdbCatalytic residuesCofactor-binding residuesModified residuescomment
1e0dA01



1eehA01



1uagA01



2uagA01



3uagA01



4uagA01



1e0dA02LYS 115;ASN 138;       
SER 116;GLU 157(Magnesium-2);                    

invisible H183
1eehA03LYS 115;ASN 138;HIS 183
SER 116;GLU 157(Magnesium-2);HIS 183(Magnesium-1)


1uagA02LYS 115;ASN 138;HIS 183
SER 116;GLU 157(Magnesium-2);HIS 183(Magnesium-1)
KCX 198(carbanated Lys)

2uagA02LYS 115;ASN 138;HIS 183
SER 116;GLU 157(Magnesium-2);HIS 183(Magnesium-1)
KCX 198(carbamated Lys)

3uagA02LYS 115;ASN 138;HIS 183
SER 116;GLU 157(Magnesium-2);HIS 183(Magnesium-1)
KCX 198(carbamated Lys)

4uagA02LYS 115;ASN 138;HIS 183
SER 116;GLU 157(Magnesium-2);HIS 183(Magnesium-1)
KCX 198(carbamated Lys)

1e0dA03



1eehA02



1uagA03



2uagA03



3uagA03



4uagA03




References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig.6, p.3422
[3]Fig.8, p.587-588

references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS).
Medline ID97361823
PubMed ID9218784
JournalEMBO J
Year1997
Volume16
Pages3416-25
AuthorsBertrand JA, Auger G, Fanchon E, Martin L, Blanot D, van Heijenoort J, Dideberg O
TitleCrystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli.
Related PDB1e0d,1uag
Related Swiss-protP14900
[2]
PubMed ID9631510
JournalProtein Expr Purif
Year1998
Volume13
Pages23-9
AuthorsAuger G, Martin L, Bertrand J, Ferrari P, Fanchon E, Vaganay S, Petillot Y, van Heijenoort J, Blanot D, Dideberg O
TitleLarge-scale preparation, purification, and crystallization of UDP-N-acetylmuramoyl-L-alanine: D-glutamate ligase from Escherichia coli.
[3]
CommentsX-ray crystallography
PubMed ID10356330
JournalJ Mol Biol
Year1999
Volume289
Pages579-90
AuthorsBertrand JA, Auger G, Martin L, Fanchon E, Blanot D, Le Beller D, van Heijenoort J, Dideberg O
TitleDetermination of the MurD mechanism through crystallographic analysis of enzyme complexes.
Related PDB2uag,3uag,4uag
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID20425115
PubMed ID10966819
JournalJ Mol Biol
Year2000
Volume301
Pages1257-66
AuthorsBertrand JA, Fanchon E, Martin L, Chantalat L, Auger G, Blanot D, van Heijenoort J, Dideberg O
Title"Open" structures of MurD: domain movements and structural similarities with folylpolyglutamate synthetase.
Related PDB1eeh
Related Swiss-protP14900
[5]
PubMed ID10970743
JournalJ Mol Biol
Year2000
Volume302
Pages427-40
AuthorsSheng Y, Sun X, Shen Y, Bognar AL, Baker EN, Smith CA
TitleStructural and functional similarities in the ADP-forming amide bond ligase superfamily: implications for a substrate-induced conformational change in folylpolyglutamate synthetase.
[6]
PubMed ID11090285
JournalJ Mol Biol
Year2000
Volume304
Pages435-45
AuthorsYan Y, Munshi S, Leiting B, Anderson MS, Chrzas J, Chen Z
TitleCrystal structure of Escherichia coli UDPMurNAc-tripeptide d-alanyl-d-alanine-adding enzyme (MurF) at 2.3 A resolution.
[7]
PubMed ID11124264
JournalJ Biol Chem
Year2001
Volume276
Pages10999-1006
AuthorsGordon E, Flouret B, Chantalat L, van Heijenoort J, Mengin-Lecreulx D, Dideberg O
TitleCrystal structure of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate: meso-diaminopimelate ligase from Escherichia coli.

comments
This enzyme catalyzes two successive transfer reactions, according to the literature [1] & [3]. Firstly, it transfers phosphate group from ATP to the carboxyl group of the second substrate, UDP-MurNAc (UMA), forming an acyl-phosphate intermediate. Secondly, it transfers acyl group (UMA) to the amine group of the other substrate, D-glutamate, releasing the inorganic phosphate.
The first reaction (phosphate transfer) occurs as follows (see [3]):
(1) The acceptor group, carboxyl oxygen atom of UMA, makes a nucleophilic attack on the transferred group, the phosphorus atom of the gamma-phosphate group of ATP. The reaction proceeds through an SN2-mechanism.
(2) Lys115 and Mg2+ at site-2 stabilize the transition-state by neutralizing the transferred and leaving group, which are the beta- and gamma-phosphate groups of ATP.
(3) Mg2+ at site-1 activates the acceptor group, the carboxyl group of UMA, and stabilizes the transferred group, the gamma-phosphate group of ATP.
The second reaction (acyl transfer) occurs as follows (see [3]):
(1') The first base, probably the gamma-phosphate group of the substrate, may abstract the proton from the second acceptor group, the amine group of D-Glu.
(2') After the third substrate, D-Glu, was bound to the active site, the acceptor group, the amine group of D-Glu, would make a nucleophilic attack on the second transferred group, the carbonyl carbon of phosphorylated-UMA, forming the tetrahedral intermediate.
(3') The second base, probably His183, may abstract the proton from the amine of the tetrahedral intermediate, facilitating the transformation of the intermediate into the final product and the release of the phosphate.

createdupdated
2004-03-252009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

© Computational Biology Research Center, AIST, 2004 All Rights Reserved.