MURD_ECOLI
ID MURD_ECOLI Reviewed; 438 AA.
AC P14900;
DT 01-APR-1990, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 210.
DE RecName: Full=UDP-N-acetylmuramoylalanine--D-glutamate ligase {ECO:0000303|PubMed:1765076};
DE EC=6.3.2.9 {ECO:0000269|PubMed:1765076};
DE AltName: Full=D-glutamic acid-adding enzyme;
DE AltName: Full=UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase;
GN Name=murD; OrderedLocusNames=b0088, JW0086;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=2179861; DOI=10.1093/nar/18.4.1058;
RA Ikeda M., Wachi M., Ishino F., Matsuhashi M.;
RT "Nucleotide sequence involving murD and an open reading frame ORF-Y spacing
RT murF and ftsW in Escherichia coli.";
RL Nucleic Acids Res. 18:1058-1058(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=2129548; DOI=10.1093/nar/18.1.183;
RA Mengin-Lecreulx D., van Heijenoort J.;
RT "Nucleotide sequence of the murD gene encoding the UDP-MurNAc-L-Ala-D-Glu
RT synthetase of Escherichia coli.";
RL Nucleic Acids Res. 18:183-183(1990).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Flouret B.;
RL Submitted (MAR-1990) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1630901; DOI=10.1093/nar/20.13.3305;
RA Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K.,
RA Mizobuchi K., Nakata A.;
RT "Systematic sequencing of the Escherichia coli genome: analysis of the 0-
RT 2.4 min region.";
RL Nucleic Acids Res. 20:3305-3308(1992).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 376-438.
RC STRAIN=K12;
RX PubMed=2509435; DOI=10.1128/jb.171.11.6375-6378.1989;
RA Ikeda M., Sato T., Wachi M., Jung H.K., Ishino F., Kobayashi Y.,
RA Matsuhashi M.;
RT "Structural similarity among Escherichia coli FtsW and RodA proteins and
RT Bacillus subtilis SpoVE protein, which function in cell division, cell
RT elongation, and spore formation, respectively.";
RL J. Bacteriol. 171:6375-6378(1989).
RN [8]
RP PROTEIN SEQUENCE OF 2-20, CATALYTIC ACTIVITY, FUNCTION, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=K12;
RX PubMed=1765076; DOI=10.1111/j.1432-1033.1991.tb16486.x;
RA Pratviel-Sosa F., Mengin-Lecreulx D., van Heijenoort J.;
RT "Over-production, purification and properties of the uridine diphosphate N-
RT acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli.";
RL Eur. J. Biochem. 202:1169-1176(1991).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS).
RX PubMed=9218784; DOI=10.1093/emboj/16.12.3416;
RA Bertrand J.A., Auger G., Fanchon E., Martin L., Blanot D.,
RA van Heijenoort J., Dideberg O.;
RT "Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
RT from Escherichia coli.";
RL EMBO J. 16:3416-3425(1997).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
RX PubMed=10966819; DOI=10.1006/jmbi.2000.3994;
RA Bertrand J.A., Fanchon E., Martin L., Chantalat L., Auger G., Blanot D.,
RA van Heijenoort J., Dideberg O.;
RT "'Open' structures of MurD: domain movements and structural similarities
RT with folylpolyglutamate synthetase.";
RL J. Mol. Biol. 301:1257-1266(2000).
CC -!- FUNCTION: Cell wall formation (Probable). Catalyzes the addition of
CC glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine
CC (UMA) (PubMed:1765076). {ECO:0000269|PubMed:1765076, ECO:0000305}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + D-glutamate + UDP-N-acetyl-alpha-D-muramoyl-L-alanine =
CC ADP + H(+) + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-
CC glutamate; Xref=Rhea:RHEA:16429, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:29986, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:83898, ChEBI:CHEBI:83900, ChEBI:CHEBI:456216; EC=6.3.2.9;
CC Evidence={ECO:0000269|PubMed:1765076};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000305|PubMed:1765076};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=7.5 uM for UDP-N-acetylmuramoyl-L-alanine
CC {ECO:0000269|PubMed:1765076};
CC KM=55 uM for D-glutamate {ECO:0000269|PubMed:1765076};
CC KM=138 uM for ATP/ Mg(2+) {ECO:0000269|PubMed:1765076};
CC Note=The optimum activity is at 11-16 mM for potassium phosphate and
CC at 5 mM for Mg(2+). {ECO:0000269|PubMed:1765076};
CC pH dependence:
CC Optimum pH is 9.0. {ECO:0000305|PubMed:1765076};
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC -!- INTERACTION:
CC P14900; P14900: murD; NbExp=3; IntAct=EBI-554780, EBI-554780;
CC P14900; P0AGG4: trxC; NbExp=2; IntAct=EBI-554780, EBI-549392;
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- SIMILARITY: Belongs to the MurCDEF family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; X51584; CAA35933.1; -; Genomic_DNA.
DR EMBL; X17609; CAA35611.1; -; Genomic_DNA.
DR EMBL; X55034; CAA38865.1; -; Genomic_DNA.
DR EMBL; M30807; AAA83858.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73199.1; -; Genomic_DNA.
DR EMBL; AP009048; BAB96656.1; -; Genomic_DNA.
DR PIR; S08396; CEECME.
DR RefSeq; NP_414630.1; NC_000913.3.
DR RefSeq; WP_000796481.1; NZ_SSZK01000004.1.
DR PDB; 1E0D; X-ray; 2.40 A; A=2-438.
DR PDB; 1EEH; X-ray; 1.90 A; A=2-438.
DR PDB; 1UAG; X-ray; 1.95 A; A=2-438.
DR PDB; 2JFF; X-ray; 1.89 A; A=2-438.
DR PDB; 2JFG; X-ray; 1.52 A; A=2-438.
DR PDB; 2JFH; X-ray; 1.97 A; A=2-438.
DR PDB; 2UAG; X-ray; 1.70 A; A=2-438.
DR PDB; 2UUO; X-ray; 2.50 A; A=2-438.
DR PDB; 2UUP; X-ray; 1.88 A; A=2-438.
DR PDB; 2VTD; X-ray; 1.94 A; A=1-438.
DR PDB; 2VTE; X-ray; 2.20 A; A=1-438.
DR PDB; 2WJP; X-ray; 1.60 A; A=2-438.
DR PDB; 2X5O; X-ray; 1.46 A; A=2-438.
DR PDB; 2XPC; X-ray; 1.49 A; A=2-438.
DR PDB; 2Y1O; X-ray; 1.49 A; A=1-438.
DR PDB; 2Y66; X-ray; 1.49 A; A=1-438.
DR PDB; 2Y67; X-ray; 1.85 A; A=1-438.
DR PDB; 2Y68; X-ray; 1.49 A; A=1-438.
DR PDB; 3UAG; X-ray; 1.77 A; A=2-438.
DR PDB; 4UAG; X-ray; 1.66 A; A=2-438.
DR PDB; 5A5E; X-ray; 1.84 A; A=2-438.
DR PDB; 5A5F; X-ray; 1.90 A; A=2-438.
DR PDBsum; 1E0D; -.
DR PDBsum; 1EEH; -.
DR PDBsum; 1UAG; -.
DR PDBsum; 2JFF; -.
DR PDBsum; 2JFG; -.
DR PDBsum; 2JFH; -.
DR PDBsum; 2UAG; -.
DR PDBsum; 2UUO; -.
DR PDBsum; 2UUP; -.
DR PDBsum; 2VTD; -.
DR PDBsum; 2VTE; -.
DR PDBsum; 2WJP; -.
DR PDBsum; 2X5O; -.
DR PDBsum; 2XPC; -.
DR PDBsum; 2Y1O; -.
DR PDBsum; 2Y66; -.
DR PDBsum; 2Y67; -.
DR PDBsum; 2Y68; -.
DR PDBsum; 3UAG; -.
DR PDBsum; 4UAG; -.
DR PDBsum; 5A5E; -.
DR PDBsum; 5A5F; -.
DR AlphaFoldDB; P14900; -.
DR SMR; P14900; -.
DR BioGRID; 4261477; 566.
DR BioGRID; 849219; 5.
DR DIP; DIP-10279N; -.
DR IntAct; P14900; 8.
DR STRING; 511145.b0088; -.
DR BindingDB; P14900; -.
DR ChEMBL; CHEMBL4732; -.
DR DrugBank; DB03801; Lysine Nz-Carboxylic Acid.
DR DrugBank; DB08112; N-({6-[(4-CYANO-2-FLUOROBENZYL)OXY]NAPHTHALEN-2-YL}SULFONYL)-D-GLUTAMIC ACID.
DR DrugBank; DB08108; N-({6-[(4-CYANOBENZYL)OXY]NAPHTHALEN-2-YL}SULFONYL)-D-GLUTAMIC ACID.
DR DrugBank; DB08106; N-[(6-butoxynaphthalen-2-yl)sulfonyl]-D-glutamic acid.
DR DrugBank; DB08105; N-[(6-butoxynaphthalen-2-yl)sulfonyl]-L-glutamic acid.
DR DrugBank; DB08107; N-{[6-(PENTYLOXY)NAPHTHALEN-2-YL]SULFONYL}-D-GLUTAMIC ACID.
DR DrugBank; DB01673; Uridine-5'-Diphosphate-N-Acetylmuramoyl-L-Alanine.
DR DrugBank; DB02314; Uridine-5'-Diphosphate-N-Acetylmuramoyl-L-Alanine-D-Glutamate.
DR jPOST; P14900; -.
DR PaxDb; P14900; -.
DR PRIDE; P14900; -.
DR EnsemblBacteria; AAC73199; AAC73199; b0088.
DR EnsemblBacteria; BAB96656; BAB96656; BAB96656.
DR GeneID; 944818; -.
DR KEGG; ecj:JW0086; -.
DR KEGG; eco:b0088; -.
DR PATRIC; fig|1411691.4.peg.2192; -.
DR EchoBASE; EB0615; -.
DR eggNOG; COG0771; Bacteria.
DR HOGENOM; CLU_032540_1_0_6; -.
DR InParanoid; P14900; -.
DR OMA; CNFENYL; -.
DR PhylomeDB; P14900; -.
DR BioCyc; EcoCyc:UDP-NACMURALA-GLU-LIG-MON; -.
DR BioCyc; MetaCyc:UDP-NACMURALA-GLU-LIG-MON; -.
DR BRENDA; 6.3.2.9; 2026.
DR SABIO-RK; P14900; -.
DR UniPathway; UPA00219; -.
DR EvolutionaryTrace; P14900; -.
DR PRO; PR:P14900; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0008764; F:UDP-N-acetylmuramoylalanine-D-glutamate ligase activity; IDA:EcoCyc.
DR GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
DR GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IDA:EcoCyc.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR Gene3D; 3.40.1190.10; -; 1.
DR Gene3D; 3.90.190.20; -; 1.
DR HAMAP; MF_00639; MurD; 1.
DR InterPro; IPR036565; Mur-like_cat_sf.
DR InterPro; IPR004101; Mur_ligase_C.
DR InterPro; IPR036615; Mur_ligase_C_dom_sf.
DR InterPro; IPR013221; Mur_ligase_cen.
DR InterPro; IPR005762; MurD.
DR Pfam; PF02875; Mur_ligase_C; 1.
DR Pfam; PF08245; Mur_ligase_M; 1.
DR SUPFAM; SSF53244; SSF53244; 1.
DR SUPFAM; SSF53623; SSF53623; 1.
DR TIGRFAMs; TIGR01087; murD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cell cycle; Cell division; Cell shape;
KW Cell wall biogenesis/degradation; Cytoplasm; Direct protein sequencing;
KW Ligase; Nucleotide-binding; Peptidoglycan synthesis; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:1765076"
FT CHAIN 2..438
FT /note="UDP-N-acetylmuramoylalanine--D-glutamate ligase"
FT /id="PRO_0000109013"
FT BINDING 112..118
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255"
FT CONFLICT 28
FT /note="R -> A (in Ref. 2; CAA35611)"
FT /evidence="ECO:0000305"
FT CONFLICT 174
FT /note="A -> T (in Ref. 2; CAA35611)"
FT /evidence="ECO:0000305"
FT CONFLICT 276..277
FT /note="AL -> RV (in Ref. 2; CAA35611)"
FT /evidence="ECO:0000305"
FT STRAND 9..12
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 15..26
FT /evidence="ECO:0007829|PDB:2X5O"
FT TURN 27..29
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 33..40
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 44..46
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 53..57
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 60..64
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 67..71
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 75..78
FT /evidence="ECO:0007829|PDB:5A5E"
FT HELIX 80..87
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 91..93
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 95..102
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 107..111
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 113..115
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 116..129
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 134..142
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 144..147
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 154..158
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 161..165
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 173..177
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 185..187
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 191..200
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 201..203
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 207..212
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 216..218
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 221..223
FT /evidence="ECO:0007829|PDB:1EEH"
FT STRAND 229..231
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 233..243
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 246..251
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 254..258
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 259..261
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 267..282
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 287..296
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 303..310
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 313..317
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 324..331
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 340..347
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 350..352
FT /evidence="ECO:0007829|PDB:1EEH"
FT HELIX 354..359
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 362..371
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 374..378
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 382..384
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 385..387
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 391..398
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 399..401
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 407..410
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 413..416
FT /evidence="ECO:0007829|PDB:2X5O"
FT TURN 417..419
FT /evidence="ECO:0007829|PDB:2X5O"
FT STRAND 420..422
FT /evidence="ECO:0007829|PDB:2X5O"
FT HELIX 423..437
FT /evidence="ECO:0007829|PDB:2X5O"
SQ SEQUENCE 438 AA; 46974 MW; 11C64782C098F761 CRC64;
MADYQGKNVV IIGLGLTGLS CVDFFLARGV TPRVMDTRMT PPGLDKLPEA VERHTGSLND
EWLMAADLIV ASPGIALAHP SLSAAADAGI EIVGDIELFC REAQAPIVAI TGSNGKSTVT
TLVGEMAKAA GVNVGVGGNI GLPALMLLDD ECELYVLELS SFQLETTSSL QAVAATILNV
TEDHMDRYPF GLQQYRAAKL RIYENAKVCV VNADDALTMP IRGADERCVS FGVNMGDYHL
NHQQGETWLR VKGEKVLNVK EMKLSGQHNY TNALAALALA DAAGLPRASS LKALTTFTGL
PHRFEVVLEH NGVRWINDSK ATNVGSTEAA LNGLHVDGTL HLLLGGDGKS ADFSPLARYL
NGDNVRLYCF GRDGAQLAAL RPEVAEQTET MEQAMRLLAP RVQPGDMVLL SPACASLDQF
KNFEQRGNEF ARLAKELG
