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UDP-N-acetylmuramoylalanine--D-glutamate ligase (EC 6.3.2.9) (D-glutamic acid-adding enzyme) (UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase)

 MURD_ECOLI              Reviewed;         438 AA.
P14900;
01-APR-1990, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 3.
28-MAR-2018, entry version 187.
RecName: Full=UDP-N-acetylmuramoylalanine--D-glutamate ligase;
EC=6.3.2.9;
AltName: Full=D-glutamic acid-adding enzyme;
AltName: Full=UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase;
Name=murD; OrderedLocusNames=b0088, JW0086;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12;
PubMed=2179861; DOI=10.1093/nar/18.4.1058;
Ikeda M., Wachi M., Ishino F., Matsuhashi M.;
"Nucleotide sequence involving murD and an open reading frame ORF-Y
spacing murF and ftsW in Escherichia coli.";
Nucleic Acids Res. 18:1058-1058(1990).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12;
PubMed=2129548; DOI=10.1093/nar/18.1.183;
Mengin-Lecreulx D., van Heijenoort J.;
"Nucleotide sequence of the murD gene encoding the UDP-MurNAc-L-Ala-D-
Glu synthetase of Escherichia coli.";
Nucleic Acids Res. 18:183-183(1990).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Flouret B.;
Submitted (MAR-1990) to the EMBL/GenBank/DDBJ databases.
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12;
PubMed=1630901; DOI=10.1093/nar/20.13.3305;
Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N.,
Isono K., Mizobuchi K., Nakata A.;
"Systematic sequencing of the Escherichia coli genome: analysis of the
0-2.4 min region.";
Nucleic Acids Res. 20:3305-3308(1992).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
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.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[7]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 376-438.
STRAIN=K12;
PubMed=2509435; DOI=10.1128/jb.171.11.6375-6378.1989;
Ikeda M., Sato T., Wachi M., Jung H.K., Ishino F., Kobayashi Y.,
Matsuhashi M.;
"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.";
J. Bacteriol. 171:6375-6378(1989).
[8]
PROTEIN SEQUENCE OF 2-20.
STRAIN=K12;
PubMed=1765076; DOI=10.1111/j.1432-1033.1991.tb16486.x;
Pratviel-Sosa F., Mengin-Lecreulx D., van Heijenoort J.;
"Over-production, purification and properties of the uridine
diphosphate N-acetylmuramoyl-L-alanine:D-glutamate ligase from
Escherichia coli.";
Eur. J. Biochem. 202:1169-1176(1991).
[9]
X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS).
PubMed=9218784; DOI=10.1093/emboj/16.12.3416;
Bertrand J.A., Auger G., Fanchon E., Martin L., Blanot D.,
van Heijenoort J., Dideberg O.;
"Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate
ligase from Escherichia coli.";
EMBO J. 16:3416-3425(1997).
[10]
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
PubMed=10966819; DOI=10.1006/jmbi.2000.3994;
Bertrand J.A., Fanchon E., Martin L., Chantalat L., Auger G.,
Blanot D., van Heijenoort J., Dideberg O.;
"'Open' structures of MurD: domain movements and structural
similarities with folylpolyglutamate synthetase.";
J. Mol. Biol. 301:1257-1266(2000).
-!- FUNCTION: Cell wall formation. Catalyzes the addition of glutamate
to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA).
-!- CATALYTIC ACTIVITY: ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine
+ D-glutamate = ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-
alanyl-D-glutamate.
-!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
-!- INTERACTION:
Self; NbExp=3; IntAct=EBI-554780, EBI-554780;
P0AGG4:trxC; NbExp=2; IntAct=EBI-554780, EBI-549392;
-!- SUBCELLULAR LOCATION: Cytoplasm.
-!- SIMILARITY: Belongs to the MurCDEF family. {ECO:0000305}.
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution (CC BY 4.0) License
-----------------------------------------------------------------------
EMBL; X51584; CAA35933.1; -; Genomic_DNA.
EMBL; X17609; CAA35611.1; -; Genomic_DNA.
EMBL; X55034; CAA38865.1; -; Genomic_DNA.
EMBL; M30807; AAA83858.1; -; Genomic_DNA.
EMBL; U00096; AAC73199.1; -; Genomic_DNA.
EMBL; AP009048; BAB96656.1; -; Genomic_DNA.
PIR; S08396; CEECME.
RefSeq; NP_414630.1; NC_000913.3.
RefSeq; WP_000796481.1; NZ_LN832404.1.
PDB; 1E0D; X-ray; 2.40 A; A=2-438.
PDB; 1EEH; X-ray; 1.90 A; A=2-438.
PDB; 1UAG; X-ray; 1.95 A; A=2-438.
PDB; 2JFF; X-ray; 1.89 A; A=2-438.
PDB; 2JFG; X-ray; 1.52 A; A=2-438.
PDB; 2JFH; X-ray; 1.97 A; A=2-438.
PDB; 2UAG; X-ray; 1.70 A; A=2-438.
PDB; 2UUO; X-ray; 2.50 A; A=2-438.
PDB; 2UUP; X-ray; 1.88 A; A=2-438.
PDB; 2VTD; X-ray; 1.94 A; A=1-438.
PDB; 2VTE; X-ray; 2.20 A; A=1-438.
PDB; 2WJP; X-ray; 1.60 A; A=2-438.
PDB; 2X5O; X-ray; 1.46 A; A=2-438.
PDB; 2XPC; X-ray; 1.49 A; A=2-438.
PDB; 2Y1O; X-ray; 1.49 A; A=1-438.
PDB; 2Y66; X-ray; 1.49 A; A=1-438.
PDB; 2Y67; X-ray; 1.85 A; A=1-438.
PDB; 2Y68; X-ray; 1.49 A; A=1-438.
PDB; 3UAG; X-ray; 1.77 A; A=2-438.
PDB; 4UAG; X-ray; 1.66 A; A=2-438.
PDB; 5A5E; X-ray; 1.84 A; A=2-438.
PDB; 5A5F; X-ray; 1.90 A; A=2-438.
PDBsum; 1E0D; -.
PDBsum; 1EEH; -.
PDBsum; 1UAG; -.
PDBsum; 2JFF; -.
PDBsum; 2JFG; -.
PDBsum; 2JFH; -.
PDBsum; 2UAG; -.
PDBsum; 2UUO; -.
PDBsum; 2UUP; -.
PDBsum; 2VTD; -.
PDBsum; 2VTE; -.
PDBsum; 2WJP; -.
PDBsum; 2X5O; -.
PDBsum; 2XPC; -.
PDBsum; 2Y1O; -.
PDBsum; 2Y66; -.
PDBsum; 2Y67; -.
PDBsum; 2Y68; -.
PDBsum; 3UAG; -.
PDBsum; 4UAG; -.
PDBsum; 5A5E; -.
PDBsum; 5A5F; -.
ProteinModelPortal; P14900; -.
SMR; P14900; -.
BioGrid; 4261477; 566.
DIP; DIP-10279N; -.
IntAct; P14900; 8.
STRING; 316385.ECDH10B_0070; -.
BindingDB; P14900; -.
ChEMBL; CHEMBL4732; -.
DrugBank; DB03801; Lysine Nz-Carboxylic Acid.
DrugBank; DB08112; N-({6-[(4-CYANO-2-FLUOROBENZYL)OXY]NAPHTHALEN-2-YL}SULFONYL)-D-GLUTAMIC ACID.
DrugBank; DB08108; N-({6-[(4-CYANOBENZYL)OXY]NAPHTHALEN-2-YL}SULFONYL)-D-GLUTAMIC ACID.
DrugBank; DB08106; N-[(6-BUTOXYNAPHTHALEN-2-YL)SULFONYL]-D-GLUTAMIC ACID.
DrugBank; DB08105; N-[(6-BUTOXYNAPHTHALEN-2-YL)SULFONYL]-L-GLUTAMIC ACID.
DrugBank; DB08107; N-{[6-(PENTYLOXY)NAPHTHALEN-2-YL]SULFONYL}-D-GLUTAMIC ACID.
DrugBank; DB01673; Uridine-5'-Diphosphate-N-Acetylmuramoyl-L-Alanine.
DrugBank; DB02314; Uridine-5'-Diphosphate-N-Acetylmuramoyl-L-Alanine-D-Glutamate.
EPD; P14900; -.
PaxDb; P14900; -.
PRIDE; P14900; -.
EnsemblBacteria; AAC73199; AAC73199; b0088.
EnsemblBacteria; BAB96656; BAB96656; BAB96656.
GeneID; 944818; -.
KEGG; ecj:JW0086; -.
KEGG; eco:b0088; -.
PATRIC; fig|1411691.4.peg.2192; -.
EchoBASE; EB0615; -.
EcoGene; EG10620; murD.
eggNOG; ENOG4105DMZ; Bacteria.
eggNOG; COG0771; LUCA.
HOGENOM; HOG000049427; -.
InParanoid; P14900; -.
KO; K01925; -.
OMA; VDKGNDY; -.
PhylomeDB; P14900; -.
BioCyc; EcoCyc:UDP-NACMURALA-GLU-LIG-MONOMER; -.
BioCyc; MetaCyc:UDP-NACMURALA-GLU-LIG-MONOMER; -.
BRENDA; 6.3.2.9; 2026.
SABIO-RK; P14900; -.
UniPathway; UPA00219; -.
EvolutionaryTrace; P14900; -.
PRO; PR:P14900; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0042802; F:identical protein binding; IPI:IntAct.
GO; GO:0008764; F:UDP-N-acetylmuramoylalanine-D-glutamate ligase activity; IDA:EcoCyc.
GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
GO; GO:0009252; P:peptidoglycan biosynthetic process; IDA:EcoCyc.
GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
Gene3D; 3.40.1190.10; -; 1.
Gene3D; 3.90.190.20; -; 1.
HAMAP; MF_00639; MurD; 1.
InterPro; IPR036565; Mur-like_cat_sf.
InterPro; IPR004101; Mur_ligase_C.
InterPro; IPR036615; Mur_ligase_C_dom_sf.
InterPro; IPR013221; Mur_ligase_cen.
InterPro; IPR005762; UDP-N-AcMur-Glu_ligase.
Pfam; PF02875; Mur_ligase_C; 1.
Pfam; PF08245; Mur_ligase_M; 1.
SUPFAM; SSF53244; SSF53244; 1.
SUPFAM; SSF53623; SSF53623; 1.
TIGRFAMs; TIGR01087; murD; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Cell cycle; Cell division; Cell shape;
Cell wall biogenesis/degradation; Complete proteome; Cytoplasm;
Direct protein sequencing; Ligase; Nucleotide-binding;
Peptidoglycan synthesis; Reference proteome.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:1765076}.
CHAIN 2 438 UDP-N-acetylmuramoylalanine--D-glutamate
ligase.
/FTId=PRO_0000109013.
NP_BIND 112 118 ATP. {ECO:0000255}.
CONFLICT 28 28 R -> A (in Ref. 2; CAA35611).
{ECO:0000305}.
CONFLICT 174 174 A -> T (in Ref. 2; CAA35611).
{ECO:0000305}.
CONFLICT 276 277 AL -> RV (in Ref. 2; CAA35611).
{ECO:0000305}.
STRAND 9 12 {ECO:0000244|PDB:2X5O}.
HELIX 15 26 {ECO:0000244|PDB:2X5O}.
TURN 27 29 {ECO:0000244|PDB:2X5O}.
STRAND 33 40 {ECO:0000244|PDB:2X5O}.
HELIX 44 46 {ECO:0000244|PDB:2X5O}.
STRAND 53 57 {ECO:0000244|PDB:2X5O}.
HELIX 60 64 {ECO:0000244|PDB:2X5O}.
STRAND 67 71 {ECO:0000244|PDB:2X5O}.
HELIX 75 78 {ECO:0000244|PDB:5A5E}.
HELIX 80 87 {ECO:0000244|PDB:2X5O}.
STRAND 91 93 {ECO:0000244|PDB:2X5O}.
HELIX 95 102 {ECO:0000244|PDB:2X5O}.
STRAND 107 111 {ECO:0000244|PDB:2X5O}.
STRAND 113 115 {ECO:0000244|PDB:2X5O}.
HELIX 116 129 {ECO:0000244|PDB:2X5O}.
STRAND 134 142 {ECO:0000244|PDB:2X5O}.
HELIX 144 147 {ECO:0000244|PDB:2X5O}.
STRAND 154 158 {ECO:0000244|PDB:2X5O}.
HELIX 161 165 {ECO:0000244|PDB:2X5O}.
STRAND 173 177 {ECO:0000244|PDB:2X5O}.
HELIX 185 187 {ECO:0000244|PDB:2X5O}.
HELIX 191 200 {ECO:0000244|PDB:2X5O}.
HELIX 201 203 {ECO:0000244|PDB:2X5O}.
STRAND 207 212 {ECO:0000244|PDB:2X5O}.
HELIX 216 218 {ECO:0000244|PDB:2X5O}.
STRAND 221 223 {ECO:0000244|PDB:1EEH}.
STRAND 229 231 {ECO:0000244|PDB:2X5O}.
STRAND 233 243 {ECO:0000244|PDB:2X5O}.
STRAND 246 251 {ECO:0000244|PDB:2X5O}.
STRAND 254 258 {ECO:0000244|PDB:2X5O}.
HELIX 259 261 {ECO:0000244|PDB:2X5O}.
HELIX 267 282 {ECO:0000244|PDB:2X5O}.
HELIX 287 296 {ECO:0000244|PDB:2X5O}.
STRAND 303 310 {ECO:0000244|PDB:2X5O}.
STRAND 313 317 {ECO:0000244|PDB:2X5O}.
HELIX 324 331 {ECO:0000244|PDB:2X5O}.
STRAND 340 347 {ECO:0000244|PDB:2X5O}.
HELIX 350 352 {ECO:0000244|PDB:1EEH}.
HELIX 354 359 {ECO:0000244|PDB:2X5O}.
STRAND 362 371 {ECO:0000244|PDB:2X5O}.
HELIX 374 378 {ECO:0000244|PDB:2X5O}.
HELIX 382 384 {ECO:0000244|PDB:2X5O}.
STRAND 385 387 {ECO:0000244|PDB:2X5O}.
HELIX 391 398 {ECO:0000244|PDB:2X5O}.
HELIX 399 401 {ECO:0000244|PDB:2X5O}.
STRAND 407 410 {ECO:0000244|PDB:2X5O}.
STRAND 413 416 {ECO:0000244|PDB:2X5O}.
TURN 417 419 {ECO:0000244|PDB:2X5O}.
STRAND 420 422 {ECO:0000244|PDB:2X5O}.
HELIX 423 437 {ECO:0000244|PDB:2X5O}.
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


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