DB code: T00109

RLCP classification	3.113.90020.1181 : Transfer
RLCP classification	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 18420	15422 15422	84726 84726	18237 18237	16761 16761	26078 26078	46143 46143
PubChem	888 888	5957 5957	5496796 5496796	57397101 611 57397101 611	6022 6022	1004 22486802 1004 22486802	449538 449538

1e0dA01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1eehA01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1uagA01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
2uagA01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
3uagA01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
4uagA01	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1e0dA02	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1eehA03	Unbound	Unbound	Bound:UMA	Unbound	Unbound	Unbound	Unbound
1uagA02	Unbound	Unbound	Bound:UMA	Unbound	Unbound	Analogue:SO4	Unbound
2uagA02	Bound:2x_MG	Unbound	Bound:UMA	Unbound	Bound:ADP	Unbound	Unbound
3uagA02	Analogue:_MN	Unbound	Bound:UMA	Unbound	Bound:ADP	Unbound	Unbound
4uagA02	Unbound	Unbound	Unbound	Unbound	Unbound	Analogue:SO4	Bound:UAG
1e0dA03	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1eehA02	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
1uagA03	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
2uagA03	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
3uagA03	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound	Unbound
4uagA03	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
1eehA01
1uagA01
2uagA01
3uagA01
4uagA01
1e0dA02	LYS 115;ASN 138;	SER 116;GLU 157(Magnesium-2);			invisible H183
1eehA03	LYS 115;ASN 138;HIS 183	SER 116;GLU 157(Magnesium-2);HIS 183(Magnesium-1)
1uagA02	LYS 115;ASN 138;HIS 183	SER 116;GLU 157(Magnesium-2);HIS 183(Magnesium-1)	KCX 198(carbanated Lys)
2uagA02	LYS 115;ASN 138;HIS 183	SER 116;GLU 157(Magnesium-2);HIS 183(Magnesium-1)	KCX 198(carbamated Lys)
3uagA02	LYS 115;ASN 138;HIS 183	SER 116;GLU 157(Magnesium-2);HIS 183(Magnesium-1)	KCX 198(carbamated Lys)
4uagA02	LYS 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
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
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.

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.

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