DB code: T00109

RLCP classification 3.113.90020.1181 : Transfer
3.1143.80000.1190 : Transfer
CATH domain 3.40.50.720 : Rossmann fold
3.40.1190.10 : UDP-N-acetylmuramoyl-L-alanine Catalytic domain
3.90.190.20 : Protein-Tyrosine Phosphatase; Chain A
E.C. 6.3.2.9
CSA 1uag
M-CSA 1uag
MACiE M0317

CATH domain Related DB codes (homologues)
3.40.1190.10 : UDP-N-acetylmuramoyl-L-alanine D00516
3.40.50.720 : Rossmann fold S00543 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
3.90.190.20 : Protein-Tyrosine Phosphatase; Chain A D00516

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P14900 UDP-N-acetylmuramoylalanine--D-glutamate ligase
EC 6.3.2.9
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase
D-glutamic acid-adding enzyme
NP_414630.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_488393.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF02875 (Mur_ligase_C)
PF08245 (Mur_ligase_M)
[Graphical View]

KEGG enzyme name
UDP-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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P14900 MURD_ECOLI ATP + UDP-N-acetylmuramoyl-L-alanine + glutamate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D- glutamate. Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00471 D-Glutamine and D-glutamate metabolism
MAP00550 Peptidoglycan biosynthesis

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C01212 C00302 C00008 C00009 C00692
E.C.
Compound Magnesium ATP UDP-N-acetylmuramoyl-L-alanine Glutamate ADP Orthophosphate UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide amino acids,amide group,carbohydrate,nucleotide amino acids,carboxyl group amine group,nucleotide phosphate group/phosphate ion amino acids,amide group,carbohydrate,carboxyl group,nucleotide ,peptide/protein
ChEBI 18420
15422
84726
18237
16761
26078
46143
PubChem 888
5957
5496796
57397101
611
6022
1004
22486802
449538
1e0dA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1eehA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1uagA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2uagA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3uagA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
4uagA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1e0dA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1eehA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:UMA Unbound Unbound Unbound Unbound
1uagA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:UMA Unbound Unbound Analogue:SO4 Unbound
2uagA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Bound:UMA Unbound Bound:ADP Unbound Unbound
3uagA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:_MN Unbound Bound:UMA Unbound Bound:ADP Unbound Unbound
4uagA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Analogue:SO4 Bound:UAG
1e0dA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1eehA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1uagA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2uagA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3uagA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
4uagA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
PDB;2uag & literature [3]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1e0dA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1eehA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1uagA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2uagA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3uagA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
4uagA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1e0dA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 115;ASN 138; SER 116;GLU 157(Magnesium-2); invisible H183
1eehA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 115;ASN 138;HIS 183 SER 116;GLU 157(Magnesium-2);HIS 183(Magnesium-1)
1uagA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 115;ASN 138;HIS 183 SER 116;GLU 157(Magnesium-2);HIS 183(Magnesium-1) KCX 198(carbanated Lys)
2uagA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 115;ASN 138;HIS 183 SER 116;GLU 157(Magnesium-2);HIS 183(Magnesium-1) KCX 198(carbamated Lys)
3uagA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 115;ASN 138;HIS 183 SER 116;GLU 157(Magnesium-2);HIS 183(Magnesium-1) KCX 198(carbamated Lys)
4uagA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 115;ASN 138;HIS 183 SER 116;GLU 157(Magnesium-2);HIS 183(Magnesium-1) KCX 198(carbamated Lys)
1e0dA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1eehA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1uagA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2uagA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3uagA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
4uagA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.6, p.3422
[3]
Fig.8, p.587-588

References
[1]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS).
Medline ID 97361823
PubMed ID 9218784
Journal EMBO J
Year 1997
Volume 16
Pages 3416-25
Authors Bertrand JA, Auger G, Fanchon E, Martin L, Blanot D, van Heijenoort J, Dideberg O
Title Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli.
Related PDB 1e0d 1uag
Related UniProtKB P14900
[2]
Resource
Comments
Medline ID
PubMed ID 9631510
Journal Protein Expr Purif
Year 1998
Volume 13
Pages 23-9
Authors Auger G, Martin L, Bertrand J, Ferrari P, Fanchon E, Vaganay S, Petillot Y, van Heijenoort J, Blanot D, Dideberg O
Title Large-scale preparation, purification, and crystallization of UDP-N-acetylmuramoyl-L-alanine: D-glutamate ligase from Escherichia coli.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10356330
Journal J Mol Biol
Year 1999
Volume 289
Pages 579-90
Authors Bertrand JA, Auger G, Martin L, Fanchon E, Blanot D, Le Beller D, van Heijenoort J, Dideberg O
Title Determination of the MurD mechanism through crystallographic analysis of enzyme complexes.
Related PDB 2uag 3uag 4uag
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID 20425115
PubMed ID 10966819
Journal J Mol Biol
Year 2000
Volume 301
Pages 1257-66
Authors Bertrand 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 PDB 1eeh
Related UniProtKB P14900
[5]
Resource
Comments
Medline ID
PubMed ID 10970743
Journal J Mol Biol
Year 2000
Volume 302
Pages 427-40
Authors Sheng Y, Sun X, Shen Y, Bognar AL, Baker EN, Smith CA
Title Structural and functional similarities in the ADP-forming amide bond ligase superfamily: implications for a substrate-induced conformational change in folylpolyglutamate synthetase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 11090285
Journal J Mol Biol
Year 2000
Volume 304
Pages 435-45
Authors Yan Y, Munshi S, Leiting B, Anderson MS, Chrzas J, Chen Z
Title Crystal structure of Escherichia coli UDPMurNAc-tripeptide d-alanyl-d-alanine-adding enzyme (MurF) at 2.3 A resolution.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 11124264
Journal J Biol Chem
Year 2001
Volume 276
Pages 10999-1006
Authors Gordon E, Flouret B, Chantalat L, van Heijenoort J, Mengin-Lecreulx D, Dideberg O
Title Crystal structure of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate: meso-diaminopimelate ligase from Escherichia coli.
Related PDB
Related UniProtKB

Comments
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.
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.
(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.

Created Updated
2004-03-25 2009-02-26