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Database: UniProt
Entry: Q9WY79
LinkDB: Q9WY79
Original site: Q9WY79 
ID   MURE_THEMA              Reviewed;         490 AA.
AC   Q9WY79;
DT   30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1999, sequence version 1.
DT   26-NOV-2014, entry version 114.
DE   RecName: Full=UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase;
DE            EC=6.3.2.37;
DE            EC=6.3.2.7;
DE   AltName: Full=D-lysine-adding enzyme;
DE   AltName: Full=L-lysine-adding enzyme;
DE   AltName: Full=UDP-MurNAc-L-Ala-D-Glu:LD-Lys ligase;
DE   AltName: Full=UDP-MurNAc-tripeptide synthetase;
DE   AltName: Full=UDP-N-acetylmuramyl-tripeptide synthetase;
GN   Name=murE; OrderedLocusNames=TM_0237;
OS   Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099).
OC   Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX   NCBI_TaxID=243274;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 43589 / MSB8 / DSM 3109 / JCM 10099;
RX   PubMed=10360571; DOI=10.1038/20601;
RA   Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J.,
RA   Haft D.H., Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A.,
RA   McDonald L.A., Utterback T.R., Malek J.A., Linher K.D., Garrett M.M.,
RA   Stewart A.M., Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L.,
RA   Heidelberg J.F., Sutton G.G., Fleischmann R.D., Eisen J.A., White O.,
RA   Salzberg S.L., Smith H.O., Venter J.C., Fraser C.M.;
RT   "Evidence for lateral gene transfer between Archaea and Bacteria from
RT   genome sequence of Thermotoga maritima.";
RL   Nature 399:323-329(1999).
RN   [2]
RP   FUNCTION, CHARACTERIZATION, SUBSTRATE SPECIFICITY, AND
RP   BIOPHYSICOCHEMICAL PROPERTIES.
RX   PubMed=16595662; DOI=10.1074/jbc.M506311200;
RA   Boniface A., Bouhss A., Mengin-Lecreulx D., Blanot D.;
RT   "The MurE synthetase from Thermotoga maritima is endowed with an
RT   unusual D-lysine adding activity.";
RL   J. Biol. Chem. 281:15680-15686(2006).
CC   -!- FUNCTION: Catalyzes the addition of both L- and D-lysine to the
CC       nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
CC       (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan.
CC       Is also able to use meso-diaminopimelate as the amino acid
CC       substrate in vitro, although much less efficiently.
CC       {ECO:0000269|PubMed:16595662}.
CC   -!- CATALYTIC ACTIVITY: ATP + UDP-N-acetylmuramoyl-L-alanyl-D-
CC       glutamate + L-lysine = ADP + phosphate + UDP-N-acetylmuramoyl-L-
CC       alanyl-D-glutamyl-L-lysine.
CC   -!- CATALYTIC ACTIVITY: ATP + UDP-N-acetylmuramoyl-L-alanyl-D-
CC       glutamate + D-lysine = ADP + phosphate + UDP-N-acetylmuramoyl-L-
CC       alanyl-D-glutamyl-D-lysine.
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=0.45 mM for UDP-N-acetylmuramoyl-L-Ala-D-Glu
CC         {ECO:0000269|PubMed:16595662};
CC         KM=2.8 mM for L-lysine (at pH 9.4)
CC         {ECO:0000269|PubMed:16595662};
CC         KM=0.65 mM for L-lysine (at pH 8) {ECO:0000269|PubMed:16595662};
CC         KM=1.7 mM for D-lysine (at pH 9.4)
CC         {ECO:0000269|PubMed:16595662};
CC         KM=1.0 mM for D-lysine (at pH 8) {ECO:0000269|PubMed:16595662};
CC         KM=4.8 mM for meso-diaminopimelate (at pH 9.4)
CC         {ECO:0000269|PubMed:16595662};
CC         KM=27 mM for L-ornithine (at pH 9.4)
CC         {ECO:0000269|PubMed:16595662};
CC         KM=3.6 mM for ATP {ECO:0000269|PubMed:16595662};
CC         Note=The catalytic efficiency for the L-lysine adding activity
CC         is 4-fold and 10-fold higher than that for the D-lysine and
CC         meso-diaminopimelate adding activity, respectively.;
CC       pH dependence:
CC         Optimum pH is 9.4 for the L-lysine adding activity.
CC         {ECO:0000269|PubMed:16595662};
CC       Temperature dependence:
CC         Optimum temperature is 68 degrees Celsius for the L-lysine
CC         adding activity. {ECO:0000269|PubMed:16595662};
CC   -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC   -!- PTM: Carbamoylation is probably crucial for Mg(2+) binding and,
CC       consequently, for the gamma-phosphate positioning of ATP.
CC       {ECO:0000250}.
CC   -!- MISCELLANEOUS: The peptidoglycan of T.maritima was shown to
CC       contain approximate amounts of both enantiomers of lysine and no
CC       diaminopimelate.
CC   -!- SIMILARITY: Belongs to the MurCDEF family. MurE subfamily.
CC       {ECO:0000305}.
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DR   EMBL; AE000512; AAD35328.1; -; Genomic_DNA.
DR   PIR; G72402; G72402.
DR   RefSeq; NP_228051.1; NC_000853.1.
DR   RefSeq; YP_007976586.1; NC_021214.1.
DR   RefSeq; YP_008990789.1; NC_023151.1.
DR   PDB; 4BUB; X-ray; 2.90 A; A/B=1-490.
DR   PDBsum; 4BUB; -.
DR   ProteinModelPortal; Q9WY79; -.
DR   STRING; 243274.TM0237; -.
DR   PRIDE; Q9WY79; -.
DR   EnsemblBacteria; AAD35328; AAD35328; TM_0237.
DR   GeneID; 18092562; -.
DR   GeneID; 897137; -.
DR   KEGG; tma:TM0237; -.
DR   PATRIC; 23935349; VBITheMar51294_0240.
DR   eggNOG; COG0769; -.
DR   InParanoid; Q9WY79; -.
DR   KO; K01928; -.
DR   OMA; KIAVDYA; -.
DR   OrthoDB; EOG6PKFCR; -.
DR   BioCyc; MetaCyc:MONOMER-16146; -.
DR   UniPathway; UPA00219; -.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-HAMAP.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-HAMAP.
DR   GO; GO:0004326; F:tetrahydrofolylpolyglutamate synthase activity; IEA:InterPro.
DR   GO; GO:0047482; F:UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase activity; IEA:UniProtKB-EC.
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; IEA:UniProtKB-HAMAP.
DR   GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR   Gene3D; 3.40.1190.10; -; 1.
DR   Gene3D; 3.40.1390.10; -; 1.
DR   Gene3D; 3.90.190.20; -; 1.
DR   HAMAP; MF_00208; MurE; 1.
DR   InterPro; IPR018109; Folylpolyglutamate_synth_CS.
DR   InterPro; IPR004101; Mur_ligase_C.
DR   InterPro; IPR013221; Mur_ligase_cen.
DR   InterPro; IPR000713; Mur_ligase_N.
DR   InterPro; IPR005761; UDP-N-AcMur-Glu-dNH2Pim_ligase.
DR   Pfam; PF01225; Mur_ligase; 1.
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   SUPFAM; SSF63418; SSF63418; 1.
DR   TIGRFAMs; TIGR01085; murE; 1.
PE   1: Evidence at protein level;
KW   3D-structure; ATP-binding; Cell cycle; Cell division; Cell shape;
KW   Cell wall biogenesis/degradation; Complete proteome; Cytoplasm;
KW   Ligase; Nucleotide-binding; Peptidoglycan synthesis;
KW   Reference proteome.
FT   CHAIN         1    490       UDP-N-acetylmuramoyl-L-alanyl-D-
FT                                glutamate--LD-lysine ligase.
FT                                /FTId=PRO_0000101962.
FT   NP_BIND     110    116       ATP. {ECO:0000255}.
FT   REGION      152    153       UDP-MurNAc-L-Ala-D-Glu binding.
FT                                {ECO:0000250}.
FT   BINDING      32     32       UDP-MurNAc-L-Ala-D-Glu. {ECO:0000250}.
FT   BINDING     179    179       UDP-MurNAc-L-Ala-D-Glu. {ECO:0000250}.
FT   BINDING     185    185       UDP-MurNAc-L-Ala-D-Glu. {ECO:0000250}.
FT   BINDING     187    187       UDP-MurNAc-L-Ala-D-Glu. {ECO:0000250}.
FT   MOD_RES     219    219       N6-carboxylysine. {ECO:0000250}.
FT   HELIX         3      9       {ECO:0000244|PDB:4BUB}.
FT   TURN         10     13       {ECO:0000244|PDB:4BUB}.
FT   STRAND       14     19       {ECO:0000244|PDB:4BUB}.
FT   STRAND       27     32       {ECO:0000244|PDB:4BUB}.
FT   STRAND       37     43       {ECO:0000244|PDB:4BUB}.
FT   HELIX        54     60       {ECO:0000244|PDB:4BUB}.
FT   STRAND       64     70       {ECO:0000244|PDB:4BUB}.
FT   STRAND       74     76       {ECO:0000244|PDB:4BUB}.
FT   STRAND       78     82       {ECO:0000244|PDB:4BUB}.
FT   HELIX        84     95       {ECO:0000244|PDB:4BUB}.
FT   TURN         99    102       {ECO:0000244|PDB:4BUB}.
FT   STRAND      103    112       {ECO:0000244|PDB:4BUB}.
FT   HELIX       114    126       {ECO:0000244|PDB:4BUB}.
FT   STRAND      133    135       {ECO:0000244|PDB:4BUB}.
FT   HELIX       156    168       {ECO:0000244|PDB:4BUB}.
FT   STRAND      172    177       {ECO:0000244|PDB:4BUB}.
FT   HELIX       182    185       {ECO:0000244|PDB:4BUB}.
FT   TURN        186    188       {ECO:0000244|PDB:4BUB}.
FT   STRAND      193    198       {ECO:0000244|PDB:4BUB}.
FT   STRAND      203    207       {ECO:0000244|PDB:4BUB}.
FT   STRAND      209    211       {ECO:0000244|PDB:4BUB}.
FT   HELIX       212    220       {ECO:0000244|PDB:4BUB}.
FT   HELIX       221    223       {ECO:0000244|PDB:4BUB}.
FT   STRAND      226    235       {ECO:0000244|PDB:4BUB}.
FT   HELIX       236    238       {ECO:0000244|PDB:4BUB}.
FT   TURN        239    241       {ECO:0000244|PDB:4BUB}.
FT   STRAND      246    254       {ECO:0000244|PDB:4BUB}.
FT   STRAND      257    261       {ECO:0000244|PDB:4BUB}.
FT   STRAND      272    276       {ECO:0000244|PDB:4BUB}.
FT   STRAND      282    285       {ECO:0000244|PDB:4BUB}.
FT   HELIX       293    305       {ECO:0000244|PDB:4BUB}.
FT   TURN        306    308       {ECO:0000244|PDB:4BUB}.
FT   HELIX       311    315       {ECO:0000244|PDB:4BUB}.
FT   TURN        316    320       {ECO:0000244|PDB:4BUB}.
FT   STRAND      327    330       {ECO:0000244|PDB:4BUB}.
FT   HELIX       332    334       {ECO:0000244|PDB:4BUB}.
FT   TURN        335    338       {ECO:0000244|PDB:4BUB}.
FT   STRAND      340    343       {ECO:0000244|PDB:4BUB}.
FT   HELIX       349    362       {ECO:0000244|PDB:4BUB}.
FT   STRAND      367    371       {ECO:0000244|PDB:4BUB}.
FT   HELIX       383    392       {ECO:0000244|PDB:4BUB}.
FT   STRAND      394    398       {ECO:0000244|PDB:4BUB}.
FT   STRAND      404    406       {ECO:0000244|PDB:4BUB}.
FT   HELIX       409    416       {ECO:0000244|PDB:4BUB}.
FT   STRAND      425    427       {ECO:0000244|PDB:4BUB}.
FT   HELIX       431    441       {ECO:0000244|PDB:4BUB}.
FT   STRAND      447    450       {ECO:0000244|PDB:4BUB}.
FT   STRAND      458    462       {ECO:0000244|PDB:4BUB}.
FT   STRAND      465    468       {ECO:0000244|PDB:4BUB}.
FT   HELIX       471    484       {ECO:0000244|PDB:4BUB}.
SQ   SEQUENCE   490 AA;  54740 MW;  21A6FBE388D741A9 CRC64;
     MNISTIVSNL KDLILEVRAP YDLEITGVSN HSSKVKKGDL FICRRGEKFD SHEIIPEVME
     KGAVAVVVER EIDLDFPYIQ VFDSRYFEAK VASLFFEDPW KDVLTFGVTG TNGKTTTTMM
     IYHMLTSLGE RGSVLTTAVK RILGNSYYDD ITTPDAITIL SAMKENREGG GKFFALEVSS
     HALVQQRVEG VRFDVGIFTN ISRDHLDFHG TFENYLKAKL HLFDLLKDDG VAVLNESLAD
     AFNRKSRKIT FGTSKNADYR LGNIEVSWEG TQFVLETPDG LLKVFTRAIG DFNAYNAAAA
     IAALHQLGYD PKDLASSLET FTGVEGRFEV VRGAKKIGLN VVVDFAHSPD ALEKLLKNVR
     KISQGRVIVV FGAGGNSDRG KRPMMSEVAS KLADVVILTT DDPRGEDPEQ IMEDLIKGID
     KRKPYLVLFD RREAIETALT IANRGDSVVI AGRGHERYQI IDEEKKVPFQ DREVVEEIIR
     DKLKGRKYAQ
//
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