P22188 (MURE_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
EC=6.3.2.13

Alternative name(s):
Meso-A2pm-adding enzyme
Meso-diaminopimelate-adding enzyme
UDP-MurNAc-L-Ala-D-Glu:meso-diaminopimelate ligase
UDP-MurNAc-tripeptide synthetase
UDP-N-acetylmuramyl-tripeptide synthetase

Gene names

Name:	murE
Ordered Locus Names:	b0085, JW0083

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	495 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	Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan. Is also able to use many meso-diaminopimelate analogs as substrates, although much less efficiently, but not L-lysine. Ref.7 Ref.8 Ref.11
Catalytic activity	ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate + meso-2,6-diaminoheptanedioate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diamino-heptanedioate. HAMAP-Rule MF_00208
Enzyme regulation	Activated by potassium phosphate. Ref.7
Pathway	Cell wall biogenesis; peptidoglycan biosynthesis. HAMAP-Rule MF_00208
Subcellular location	Cytoplasm Probable HAMAP-Rule MF_00208.
Post-translational modification	Carbamoylation is probably crucial for Mg2+ binding and, consequently, for the gamma-phosphate positioning of ATP. HAMAP-Rule MF_00208
Sequence similarities	Belongs to the MurCDEF family. MurE subfamily.
Biophysicochemical properties	Kinetic parameters: KM=76 µM for UDP-N-acetylmuramoyl-L-Ala-D-Glu Ref.7 Ref.9 KM=36 µM for meso-diaminopimelate KM=1500 µM for meso-lanthionine KM=3900 µM for L-allo-cystathionine KM=10000 µM for D-allo-cystathionine KM=620 µM for ATP Vmax=32 nmol/min/mg enzyme with meso-diaminopimelate as substrate Vmax=23 nmol/min/mg enzyme with meso-lanthionine as substrate Vmax=19 nmol/min/mg enzyme with L-allo-cystathionine as substrate Vmax=23 nmol/min/mg enzyme with L-allo-cystathionine as substrate pH dependence: Optimum pH is about 8.

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 peptidoglycan biosynthetic process Inferred from electronic annotation. Source: HAMAP regulation of cell shape Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase activity Inferred from direct assay Ref.7. Source: EcoliWiki UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
carA	P0A6F1	1	EBI-553061,EBI-546107

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.6 Ref.7

Chain

2 – 495

494

UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase HAMAP-Rule MF_00208

PRO_0000101893

Regions

Nucleotide binding

116 – 122

7

ATP Potential

Region

44 – 46

3

UDP-MurNAc-L-Ala-D-Glu binding HAMAP-Rule MF_00208

Region

158 – 159

2

UDP-MurNAc-L-Ala-D-Glu binding HAMAP-Rule MF_00208

Region

414 – 417

4

Meso-diaminopimelate binding HAMAP-Rule MF_00208

Motif

414 – 417

4

Meso-diaminopimelate recognition motif HAMAP-Rule MF_00208

Sites

Binding site

27

1

UDP-MurNAc-L-Ala-D-Glu; via carbonyl oxygen

Binding site

29

1

UDP-MurNAc-L-Ala-D-Glu

Binding site

157

1

UDP-MurNAc-L-Ala-D-Glu

Binding site

185

1

UDP-MurNAc-L-Ala-D-Glu

Binding site

191

1

UDP-MurNAc-L-Ala-D-Glu

Binding site

193

1

UDP-MurNAc-L-Ala-D-Glu

Binding site

390

1

Meso-diaminopimelate

Binding site

465

1

Meso-diaminopimelate; via carbonyl oxygen

Binding site

469

1

Meso-diaminopimelate

Amino acid modifications

Modified residue

225

1

N6-carboxylysine HAMAP-Rule MF_00208

Natural variations

Natural variant

344

1

E → K in murE1.

Natural variant

495

1

A → S in murE1.

Secondary structure

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495

Helix Strand Turn

Details...

Helix

6 – 10

5

Turn

11 – 13

3

Beta strand

25 – 27

3

Helix

29 – 31

3

Beta strand

37 – 40

4

Helix

48 – 51

4

Helix

52 – 57

6

Beta strand

61 – 66

6

Turn

68 – 70

3

Beta strand

76 – 79

4

Beta strand

82 – 87

6

Helix

90 – 101

12

Helix

105 – 107

3

Beta strand

108 – 118

11

Helix

120 – 133

14

Beta strand

138 – 142

5

Beta strand

145 – 148

4

Beta strand

156 – 159

4

Helix

162 – 174

13

Beta strand

179 – 183

5

Helix

186 – 190

5

Turn

191 – 196

6

Beta strand

200 – 204

5

Helix

212 – 215

4

Helix

218 – 230

13

Beta strand

236 – 240

5

Helix

244 – 250

7

Beta strand

257 – 263

7

Turn

267 – 269

3

Beta strand

271 – 281

11

Beta strand

286 – 292

7

Beta strand

297 – 301

5

Helix

306 – 321

16

Helix

326 – 332

7

Helix

333 – 335

3

Beta strand

342 – 346

5

Beta strand

353 – 357

5

Helix

362 – 374

13

Beta strand

380 – 384

5

Beta strand

388 – 390

3

Helix

394 – 405

12

Beta strand

407 – 411

5

Helix

421 – 429

9

Helix

435 – 437

3

Beta strand

438 – 440

3

Helix

444 – 454

11

Beta strand

460 – 465

6

Beta strand

471 – 474

4

Beta strand

477 – 480

4

Helix

483 – 491

9

Sequences

	Sequence		Length	Mass (Da)
	P22188 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: D4A7A3E56D6C7E49	FASTA	495	53,344
	10 20 30 40 50 60 MADRNLRDLL APWVPDAPSR ALREMTLDSR VAAAGDLFVA VVGHQADGRR YIPQAIAQGV 70 80 90 100 110 120 AAIIAEAKDE ATDGEIREMH GVPVIYLSQL NERLSALAGR FYHEPSDNLR LVGVTGTNGK 130 140 150 160 170 180 TTTTQLLAQW SQLLGEISAV MGTVGNGLLG KVIPTENTTG SAVDVQHELA GLVDQGATFC 190 200 210 220 230 240 AMEVSSHGLV QHRVAALKFA ASVFTNLSRD HLDYHGDMEH YEAAKWLLYS EHHCGQAIIN 250 260 270 280 290 300 ADDEVGRRWL AKLPDAVAVS MEDHINPNCH GRWLKATEVN YHDSGATIRF SSSWGDGEIE 310 320 330 340 350 360 SHLMGAFNVS NLLLALATLL ALGYPLADLL KTAARLQPVC GRMEVFTAPG KPTVVVDYAH 370 380 390 400 410 420 TPDALEKALQ AARLHCAGKL WCVFGCGGDR DKGKRPLMGA IAEEFADVAV VTDDNPRTEE 430 440 450 460 470 480 PRAIINDILA GMLDAGHAKV MEGRAEAVTC AVMQAKENDV VLVAGKGHED YQIVGNQRLD 490 YSDRVTVARL LGVIA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of the murE gene of Escherichia coli." Tao J.-S., Ishiguro E.E. Can. J. Microbiol. 35:1051-1054(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12.
[3]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Conditionally lethal Escherichia coli murein mutants contain point defects that map to regions conserved among murein and folyl poly-gamma-glutamate ligases: identification of a ligase superfamily." Eveland S.S., Pompliano D.L., Anderson M.S. Biochemistry 36:6223-6229(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTANT MURE1. Strain: CGSC 5989.
[6]	"Revised interpretation of the sequence containing the murE gene encoding the UDP-N-acetylmuramyl-tripeptide synthetase of Escherichia coli." Michaud C., Parquet C., Flouret B., Blanot D., van Heijenoort J. Biochem. J. 269:277-278(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-124, PROTEIN SEQUENCE OF 2-19, SEQUENCE REVISION.
[7]	"Over-production, purification and properties of the uridine-diphosphate-N-acetylmuramoyl-L-alanyl-D-glutamate: meso-2,6-diaminopimelate ligase from Escherichia coli." Michaud C., Mengin-Lecreulx D., van Heijenoort J., Blanot D. Eur. J. Biochem. 194:853-861(1990) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-19, FUNCTION, CHARACTERIZATION, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBSTRATE SPECIFICITY.
[8]	"Specificity of the uridine-diphosphate-N-acetylmuramyl-L-alanyl-D-glutamate:meso-2,6-diaminopimelate synthetase from Escherichia coli." Abo-Ghalia M., Michaud C., Blanot D., van Heijenoort J. Eur. J. Biochem. 153:81-87(1985) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBSTRATE SPECIFICITY.
[9]	"Replacement of diaminopimelic acid by cystathionine or lanthionine in the peptidoglycan of Escherichia coli." Mengin-Lecreulx D., Blanot D., van Heijenoort J. J. Bacteriol. 176:4321-4327(1994) [PubMed] [Europe PMC] [Abstract] Cited for: KINETIC PARAMETERS, SUBSTRATE SPECIFICITY.
[10]	"Escherichia coli proteome analysis using the gene-protein database." VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C. Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY 2D-GEL.
[11]	"Crystal structure of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate: meso-diaminopimelate ligase from Escherichia coli." Gordon E., Flouret B., Chantalat L., van Heijenoort J., Mengin-Lecreulx D., Dideberg O. J. Biol. Chem. 276:10999-11006(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH PRODUCT, FUNCTION, CARBAMOYLATION AT LYS-225.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X55814 Genomic DNA. Translation: CAA39334.1.
X55034 Genomic DNA. Translation: CAA38862.1.
U00096 Genomic DNA. Translation: AAC73196.1.
AP009048 Genomic DNA. Translation: BAB96653.1.
U67894 Genomic DNA. Translation: AAB60789.1.

PIR

S14384.

RefSeq

NP_414627.1. NC_000913.2.
YP_488390.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1E8C	X-ray	2.00	A/B	2-495	[»]

ProteinModelPortal

P22188.

SMR

P22188. Positions 3-495.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10280N.

IntAct

P22188. 15 interactions.

MINT

MINT-1230964.

STRING

511145.b0085.

2D gel databases

SWISS-2DPAGE

P22188.

Proteomic databases

PaxDb

P22188.

PRIDE

P22188.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73196; AAC73196; b0085.
BAB96653; BAB96653; BAB96653.

GeneID

12932647.
944791.

KEGG

ecj:Y75_p0084.
eco:b0085.

PATRIC

32115275. VBIEscCol129921_0089.

Organism-specific databases

EchoBASE

EB0616.

EcoGene

EG10621. murE.

Phylogenomic databases

eggNOG

COG0769.

HOGENOM

HOG000268118.

KO

K01928.

OMA

GALAYVD.

ProtClustDB

PRK00139.

Enzyme and pathway databases

BioCyc

EcoCyc:UDP-NACMURALGLDAPLIG-MONOMER.
ECOL316407:JW0083-MONOMER.
MetaCyc:UDP-NACMURALGLDAPLIG-MONOMER.

UniPathway

UPA00219.

Gene expression databases

Genevestigator

P22188.

Family and domain databases

Gene3D

3.40.1190.10. 1 hit.
3.90.190.20. 1 hit.

HAMAP

MF_00208. MurE.

InterPro

IPR004101. Mur_ligase_C.
IPR013221. Mur_ligase_cen.
IPR000713. Mur_ligase_N.
IPR005761. UDP-N-AcMur-Glu-dNH2Pim_ligase.
[Graphical view]

Pfam

PF01225. Mur_ligase. 1 hit.
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

TIGR01085. murE. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P22188.

Entry information

Entry name

MURE_ECOLI

Accession

Primary (citable) accession number: P22188
Secondary accession number(s): O07101

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1991
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 132 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program