P14900 (MURD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
UDP-N-acetylmuramoylalanine--D-glutamate ligase
EC=6.3.2.9

Alternative name(s):
D-glutamic acid-adding enzyme
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase

Gene names

Name:	murD
Ordered Locus Names:	b0088, JW0086

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	438 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). HAMAP MF_00639
Catalytic activity	ATP + UDP-N-acetylmuramoyl-L-alanine + glutamate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate. HAMAP MF_00639
Pathway	Cell wall biogenesis; peptidoglycan biosynthesis. HAMAP MF_00639
Subcellular location	Cytoplasm HAMAP MF_00639.
Sequence similarities	Belongs to the MurCDEF family.

Ontologies

Keywords
Biological process	Cell cycle Cell division Cell shape Cell wall biogenesis/degradation Peptidoglycan synthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Nucleotide-binding
Molecular function	Ligase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	cell cycle Inferred from electronic annotation. Source: UniProtKB-KW cell division Inferred from electronic annotation. Source: UniProtKB-KW cellular cell wall organization Inferred from electronic annotation. Source: UniProtKB-KW peptidoglycan biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW regulation of cell shape Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from direct assay Ref.8. Source: EcoliWiki
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW UDP-N-acetylmuramoylalanine-D-glutamate ligase activity Inferred from direct assay Ref.8. Source: EcoCyc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
slyD	P0A9K9	1	EBI-554780,EBI-369251
trxC	P0AGG4	1	EBI-554780,EBI-549392

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.8

Chain

2 – 438

437

UDP-N-acetylmuramoylalanine--D-glutamate ligase HAMAP MF_00639

PRO_0000109013

Regions

Nucleotide binding

112 – 118

7

ATP Potential

Experimental info

Sequence conflict

28

1

R → A in CAA35611. Ref.2

Sequence conflict

174

1

A → T in CAA35611. Ref.2

Sequence conflict

276 – 277

2

AL → RV in CAA35611. Ref.2

Secondary structure

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438

Helix Strand Turn

Details...

Beta strand

9 – 12

4

Helix

16 – 26

11

Turn

27 – 29

3

Beta strand

33 – 40

8

Helix

42 – 46

5

Beta strand

53 – 57

5

Helix

60 – 64

5

Beta strand

67 – 71

5

Helix

75 – 78

4

Helix

80 – 87

8

Beta strand

91 – 93

3

Helix

95 – 102

8

Beta strand

107 – 111

5

Beta strand

113 – 115

3

Helix

116 – 129

14

Beta strand

134 – 142

9

Helix

144 – 147

4

Beta strand

154 – 158

5

Helix

161 – 165

5

Beta strand

173 – 177

5

Helix

192 – 200

9

Helix

201 – 203

3

Beta strand

207 – 212

6

Helix

216 – 218

3

Beta strand

229 – 243

15

Beta strand

246 – 251

6

Beta strand

254 – 258

5

Helix

259 – 261

3

Helix

267 – 282

16

Helix

287 – 296

10

Beta strand

303 – 310

8

Beta strand

313 – 317

5

Helix

324 – 331

8

Beta strand

340 – 344

5

Helix

354 – 357

4

Beta strand

364 – 369

6

Helix

374 – 379

6

Turn

382 – 384

3

Helix

391 – 398

8

Turn

399 – 401

3

Beta strand

407 – 410

4

Beta strand

413 – 415

3

Helix

423 – 437

15

Sequences

	Sequence		Length	Mass (Da)
	P14900 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 11C64782C098F761	FASTA	438	46,974
	10 20 30 40 50 60 MADYQGKNVV IIGLGLTGLS CVDFFLARGV TPRVMDTRMT PPGLDKLPEA VERHTGSLND 70 80 90 100 110 120 EWLMAADLIV ASPGIALAHP SLSAAADAGI EIVGDIELFC REAQAPIVAI TGSNGKSTVT 130 140 150 160 170 180 TLVGEMAKAA GVNVGVGGNI GLPALMLLDD ECELYVLELS SFQLETTSSL QAVAATILNV 190 200 210 220 230 240 TEDHMDRYPF GLQQYRAAKL RIYENAKVCV VNADDALTMP IRGADERCVS FGVNMGDYHL 250 260 270 280 290 300 NHQQGETWLR VKGEKVLNVK EMKLSGQHNY TNALAALALA DAAGLPRASS LKALTTFTGL 310 320 330 340 350 360 PHRFEVVLEH NGVRWINDSK ATNVGSTEAA LNGLHVDGTL HLLLGGDGKS ADFSPLARYL 370 380 390 400 410 420 NGDNVRLYCF GRDGAQLAAL RPEVAEQTET MEQAMRLLAP RVQPGDMVLL SPACASLDQF 430 KNFEQRGNEF ARLAKELG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence involving murD and an open reading frame ORF-Y spacing murF and ftsW in Escherichia coli." Ikeda M., Wachi M., Ishino F., Matsuhashi M. Nucleic Acids Res. 18:1058-1058(1990) [PubMed: 2179861] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"Nucleotide sequence of the murD gene encoding the UDP-MurNAc-L-Ala-D-Glu synthetase of Escherichia coli." Mengin-Lecreulx D., van Heijenoort J. Nucleic Acids Res. 18:183-183(1990) [PubMed: 2129548] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[3]	Flouret B. Submitted (MAR-1990) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region." Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A. Nucleic Acids Res. 20:3305-3308(1992) [PubMed: 1630901] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12.
[5]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[6]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"Structural similarity among Escherichia coli FtsW and RodA proteins and Bacillus subtilis SpoVE protein, which function in cell division, cell elongation, and spore formation, respectively." Ikeda M., Sato T., Wachi M., Jung H.K., Ishino F., Kobayashi Y., Matsuhashi M. J. Bacteriol. 171:6375-6378(1989) [PubMed: 2509435] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 376-438. Strain: K12.
[8]	"Over-production, purification and properties of the uridine diphosphate N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli." Pratviel-Sosa F., Mengin-Lecreulx D., van Heijenoort J. Eur. J. Biochem. 202:1169-1176(1991) [PubMed: 1765076] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-20. Strain: K12.
[9]	"Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli." Bertrand J.A., Auger G., Fanchon E., Martin L., Blanot D., van Heijenoort J., Dideberg O. EMBO J. 16:3416-3425(1997) [PubMed: 9218784] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS).
[10]	"'Open' structures of MurD: domain movements and structural similarities with folylpolyglutamate synthetase." Bertrand J.A., Fanchon E., Martin L., Chantalat L., Auger G., Blanot D., van Heijenoort J., Dideberg O. J. Mol. Biol. 301:1257-1266(2000) [PubMed: 10966819] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X51584 Genomic DNA. Translation: CAA35933.1.
X17609 Genomic DNA. Translation: CAA35611.1.
X55034 Genomic DNA. Translation: CAA38865.1.
M30807 Genomic DNA. Translation: AAA83858.1.
U00096 Genomic DNA. Translation: AAC73199.1.
AP009048 Genomic DNA. Translation: BAB96656.1.

PIR

CEECME. S08396.

RefSeq

NP_414630.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1E0D	X-ray	2.40	A	2-438	[»]
1EEH	X-ray	1.90	A	2-438	[»]
1UAG	X-ray	1.95	A	2-438	[»]
2JFF	X-ray	1.89	A	2-437	[»]
2JFG	X-ray	1.52	A	2-437	[»]
2JFH	X-ray	1.97	A	2-437	[»]
2UAG	X-ray	1.70	A	2-437	[»]
2UUO	X-ray	2.50	A	2-437	[»]
2UUP	X-ray	1.88	A	2-437	[»]
2VTD	X-ray	1.94	A	1-438	[»]
2VTE	X-ray	2.20	A	1-438	[»]
2WJP	X-ray	1.60	A	2-438	[»]
2X5O	X-ray	1.46	A	2-438	[»]
2XPC	X-ray	1.49	A	2-438	[»]
2Y66	X-ray	1.49	A	1-438	[»]
2Y67	X-ray	1.85	A	1-438	[»]
2Y68	X-ray	1.49	A	1-438	[»]
3UAG	X-ray	1.77	A	2-437	[»]
4UAG	X-ray	1.66	A	2-438	[»]

ProteinModelPortal

P14900.

SMR

P14900. Positions 2-438.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10279N.

IntAct

P14900. 4 interactions.

MINT

MINT-1269366.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000003340; EBESCP00000003340; EBESCG00000002737.
EBESCT00000003341; EBESCP00000003341; EBESCG00000002737.
EBESCT00000003342; EBESCP00000003342; EBESCG00000002737.
EBESCT00000003343; EBESCP00000003343; EBESCG00000002737.
EBESCT00000016281; EBESCP00000015572; EBESCG00000015341.

GeneID

944818.

GenomeReviews

Gene locus JW0086 in contig AP009048_GR.
Gene locus b0088 in contig U00096_GR.

KEGG

ecj:JW0086.
eco:b0088.

PATRIC

32115281. VBIEscCol129921_0092.

Organism-specific databases

EchoBASE

EB0615.

EcoGene

EG10620. murD.

Phylogenomic databases

eggNOG

COG0771.

GeneTree

EBGT00050000009066.

HOGENOM

HBG750024.

OMA

ACASWDM.

PhylomeDB

P14900.

ProtClustDB

PRK03806.

Enzyme and pathway databases

BioCyc

EcoCyc:UDP-NACMURALA-GLU-LIG-MONOMER.
MetaCyc:UDP-NACMURALA-GLU-LIG-MONOMER.

Gene expression databases

Genevestigator

P14900.

Family and domain databases

HAMAP

MF_00639. MurD.
[Tree]

InterPro

IPR004101. Mur_ligase_C.
IPR013221. Mur_ligase_cen.
IPR016040. NAD(P)-bd_dom.
IPR005762. UDP-N-AcMur-Glu_ligase.
[Graphical view]

Gene3D

G3DSA:3.90.190.20. Mur_ligase_C. 1 hit.
G3DSA:3.40.1190.10. Mur_ligase_cen. 1 hit.
G3DSA:3.40.50.720. NAD(P)-bd. 1 hit.

KO

K01925.

PANTHER

PTHR23135:SF2. PTHR23135:SF2. 1 hit.

Pfam

PF02875. Mur_ligase_C. 1 hit.
PF08245. Mur_ligase_M. 1 hit.
[Graphical view]

SUPFAM

SSF53244. Mur_ligase_C. 1 hit.
SSF53623. Mur_ligase_cen. 1 hit.

TIGRFAMs

TIGR01087. MurD. 1 hit.

ProtoNet

Search...

Entry information

Entry name

MURD_ECOLI

Accession

Primary (citable) accession number: P14900

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1990
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 133 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program