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P14900

- MURD_ECOLI

UniProt

P14900 - MURD_ECOLI

Protein

UDP-N-acetylmuramoylalanine--D-glutamate ligase

Gene

murD

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 157 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA).

    Catalytic activityi

    ATP + UDP-N-acetylmuramoyl-L-alanine + glutamate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate.

    Pathwayi

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi112 – 1187ATPSequence Analysis

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-HAMAP
    2. identical protein binding Source: IntAct
    3. UDP-N-acetylmuramoylalanine-D-glutamate ligase activity Source: EcoCyc

    GO - Biological processi

    1. cell cycle Source: UniProtKB-KW
    2. cell division Source: UniProtKB-KW
    3. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
    4. regulation of cell shape Source: UniProtKB-KW

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Cell cycle, Cell division, Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:UDP-NACMURALA-GLU-LIG-MONOMER.
    ECOL316407:JW0086-MONOMER.
    MetaCyc:UDP-NACMURALA-GLU-LIG-MONOMER.
    SABIO-RKP14900.
    UniPathwayiUPA00219.

    Names & Taxonomyi

    Protein namesi
    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 namesi
    Name:murD
    Ordered Locus Names:b0088, JW0086
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10620. murD.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: EcoliWiki

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 438437UDP-N-acetylmuramoylalanine--D-glutamate ligasePRO_0000109013Add
    BLAST

    Proteomic databases

    PaxDbiP14900.
    PRIDEiP14900.

    Expressioni

    Gene expression databases

    GenevestigatoriP14900.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself3EBI-554780,EBI-554780

    Protein-protein interaction databases

    DIPiDIP-10279N.
    IntActiP14900. 8 interactions.
    MINTiMINT-1269366.
    STRINGi511145.b0088.

    Structurei

    Secondary structure

    1
    438
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi9 – 124
    Helixi15 – 2612
    Turni27 – 293
    Beta strandi33 – 408
    Helixi44 – 463
    Beta strandi53 – 575
    Helixi60 – 645
    Beta strandi67 – 715
    Helixi75 – 784
    Helixi80 – 878
    Beta strandi91 – 933
    Helixi95 – 1028
    Beta strandi107 – 1115
    Beta strandi113 – 1153
    Helixi116 – 12914
    Beta strandi134 – 1429
    Helixi144 – 1474
    Beta strandi154 – 1585
    Helixi161 – 1655
    Beta strandi173 – 1775
    Helixi185 – 1873
    Helixi191 – 20010
    Helixi201 – 2033
    Beta strandi207 – 2126
    Helixi216 – 2183
    Beta strandi221 – 2233
    Beta strandi229 – 2313
    Beta strandi233 – 24311
    Beta strandi246 – 2516
    Beta strandi254 – 2585
    Helixi259 – 2613
    Helixi267 – 28216
    Helixi287 – 29610
    Beta strandi303 – 3108
    Beta strandi313 – 3175
    Helixi324 – 3318
    Beta strandi340 – 3478
    Helixi350 – 3523
    Helixi354 – 3596
    Beta strandi362 – 37110
    Helixi374 – 3785
    Helixi382 – 3843
    Beta strandi385 – 3873
    Helixi391 – 3988
    Helixi399 – 4013
    Beta strandi407 – 4104
    Beta strandi413 – 4164
    Turni417 – 4193
    Beta strandi420 – 4223
    Helixi423 – 43715

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1E0DX-ray2.40A2-438[»]
    1EEHX-ray1.90A2-438[»]
    1UAGX-ray1.95A2-438[»]
    2JFFX-ray1.89A2-438[»]
    2JFGX-ray1.52A2-438[»]
    2JFHX-ray1.97A2-438[»]
    2UAGX-ray1.70A2-438[»]
    2UUOX-ray2.50A2-438[»]
    2UUPX-ray1.88A2-438[»]
    2VTDX-ray1.94A1-438[»]
    2VTEX-ray2.20A1-438[»]
    2WJPX-ray1.60A2-438[»]
    2X5OX-ray1.46A2-438[»]
    2XPCX-ray1.49A2-438[»]
    2Y1OX-ray1.49A1-438[»]
    2Y66X-ray1.49A1-438[»]
    2Y67X-ray1.85A1-438[»]
    2Y68X-ray1.49A1-438[»]
    3UAGX-ray1.77A2-438[»]
    4UAGX-ray1.66A2-438[»]
    ProteinModelPortaliP14900.
    SMRiP14900. Positions 2-438.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP14900.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the MurCDEF family.Curated

    Phylogenomic databases

    eggNOGiCOG0771.
    HOGENOMiHOG000049427.
    KOiK01925.
    OMAiYCFGQDG.
    OrthoDBiEOG6PKFCR.
    PhylomeDBiP14900.

    Family and domain databases

    Gene3Di3.40.1190.10. 1 hit.
    3.40.50.720. 1 hit.
    3.90.190.20. 1 hit.
    HAMAPiMF_00639. MurD.
    InterProiIPR004101. Mur_ligase_C.
    IPR013221. Mur_ligase_cen.
    IPR016040. NAD(P)-bd_dom.
    IPR005762. UDP-N-AcMur-Glu_ligase.
    [Graphical view]
    PfamiPF02875. Mur_ligase_C. 1 hit.
    PF08245. Mur_ligase_M. 1 hit.
    [Graphical view]
    SUPFAMiSSF53244. SSF53244. 1 hit.
    SSF53623. SSF53623. 1 hit.
    TIGRFAMsiTIGR01087. murD. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P14900-1 [UniParc]FASTAAdd to Basket

    « Hide

    MADYQGKNVV IIGLGLTGLS CVDFFLARGV TPRVMDTRMT PPGLDKLPEA    50
    VERHTGSLND EWLMAADLIV ASPGIALAHP SLSAAADAGI EIVGDIELFC 100
    REAQAPIVAI TGSNGKSTVT TLVGEMAKAA GVNVGVGGNI GLPALMLLDD 150
    ECELYVLELS SFQLETTSSL QAVAATILNV TEDHMDRYPF GLQQYRAAKL 200
    RIYENAKVCV VNADDALTMP IRGADERCVS FGVNMGDYHL NHQQGETWLR 250
    VKGEKVLNVK EMKLSGQHNY TNALAALALA DAAGLPRASS LKALTTFTGL 300
    PHRFEVVLEH NGVRWINDSK ATNVGSTEAA LNGLHVDGTL HLLLGGDGKS 350
    ADFSPLARYL NGDNVRLYCF GRDGAQLAAL RPEVAEQTET MEQAMRLLAP 400
    RVQPGDMVLL SPACASLDQF KNFEQRGNEF ARLAKELG 438
    Length:438
    Mass (Da):46,974
    Last modified:January 23, 2007 - v3
    Checksum:i11C64782C098F761
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti28 – 281R → A in CAA35611. (PubMed:2129548)Curated
    Sequence conflicti174 – 1741A → T in CAA35611. (PubMed:2129548)Curated
    Sequence conflicti276 – 2772AL → RV in CAA35611. (PubMed:2129548)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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.
    PIRiS08396. CEECME.
    RefSeqiNP_414630.1. NC_000913.3.
    YP_488393.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73199; AAC73199; b0088.
    BAB96656; BAB96656; BAB96656.
    GeneIDi12932483.
    944818.
    KEGGiecj:Y75_p0087.
    eco:b0088.
    PATRICi32115281. VBIEscCol129921_0092.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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 .
    PIRi S08396. CEECME.
    RefSeqi NP_414630.1. NC_000913.3.
    YP_488393.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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 2-438 [» ]
    2JFG X-ray 1.52 A 2-438 [» ]
    2JFH X-ray 1.97 A 2-438 [» ]
    2UAG X-ray 1.70 A 2-438 [» ]
    2UUO X-ray 2.50 A 2-438 [» ]
    2UUP X-ray 1.88 A 2-438 [» ]
    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 [» ]
    2Y1O X-ray 1.49 A 1-438 [» ]
    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 2-438 [» ]
    4UAG X-ray 1.66 A 2-438 [» ]
    ProteinModelPortali P14900.
    SMRi P14900. Positions 2-438.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10279N.
    IntActi P14900. 8 interactions.
    MINTi MINT-1269366.
    STRINGi 511145.b0088.

    Chemistry

    BindingDBi P14900.
    ChEMBLi CHEMBL4732.

    Proteomic databases

    PaxDbi P14900.
    PRIDEi P14900.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73199 ; AAC73199 ; b0088 .
    BAB96656 ; BAB96656 ; BAB96656 .
    GeneIDi 12932483.
    944818.
    KEGGi ecj:Y75_p0087.
    eco:b0088.
    PATRICi 32115281. VBIEscCol129921_0092.

    Organism-specific databases

    EchoBASEi EB0615.
    EcoGenei EG10620. murD.

    Phylogenomic databases

    eggNOGi COG0771.
    HOGENOMi HOG000049427.
    KOi K01925.
    OMAi YCFGQDG.
    OrthoDBi EOG6PKFCR.
    PhylomeDBi P14900.

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci EcoCyc:UDP-NACMURALA-GLU-LIG-MONOMER.
    ECOL316407:JW0086-MONOMER.
    MetaCyc:UDP-NACMURALA-GLU-LIG-MONOMER.
    SABIO-RK P14900.

    Miscellaneous databases

    EvolutionaryTracei P14900.
    PROi P14900.

    Gene expression databases

    Genevestigatori P14900.

    Family and domain databases

    Gene3Di 3.40.1190.10. 1 hit.
    3.40.50.720. 1 hit.
    3.90.190.20. 1 hit.
    HAMAPi MF_00639. MurD.
    InterProi IPR004101. Mur_ligase_C.
    IPR013221. Mur_ligase_cen.
    IPR016040. NAD(P)-bd_dom.
    IPR005762. UDP-N-AcMur-Glu_ligase.
    [Graphical view ]
    Pfami PF02875. Mur_ligase_C. 1 hit.
    PF08245. Mur_ligase_M. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53244. SSF53244. 1 hit.
    SSF53623. SSF53623. 1 hit.
    TIGRFAMsi TIGR01087. murD. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12.
    5. 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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).

    Entry informationi

    Entry nameiMURD_ECOLI
    AccessioniPrimary (citable) accession number: P14900
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1990
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 157 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3