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P82974

- AMPD_CITFR

UniProt

P82974 - AMPD_CITFR

Protein

1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD

Gene

ampD

Organism
Citrobacter freundii
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 67 (01 Oct 2014)
      Sequence version 1 (02 Nov 2001)
      Previous versions | rss
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    Functioni

    Involved in both cell wall peptidoglycans recycling and beta-lactamase induction. Specifically cleaves the amide bond between the lactyl group of N-acetylmuramic acid and the alpha-amino group of the L-alanine in degradation products containing an anhydro N-acetylmuramyl moiety.1 Publication

    Catalytic activityi

    Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides.

    Cofactori

    Zinc; required for amidase activity.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi34 – 341Zinc; catalytic
    Active sitei116 – 1161Proton acceptorBy similarity
    Metal bindingi154 – 1541Zinc; catalytic
    Sitei162 – 1621Transition state stabilizerBy similarity
    Metal bindingi164 – 1641Zinc; catalytic

    GO - Molecular functioni

    1. metal ion binding Source: UniProtKB-KW
    2. N-acetylmuramoyl-L-alanine amidase activity Source: UniProtKB-EC

    GO - Biological processi

    1. peptidoglycan catabolic process Source: InterPro

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Cell wall biogenesis/degradation

    Keywords - Ligandi

    Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD (EC:3.5.1.28)
    Alternative name(s):
    N-acetylmuramoyl-L-alanine amidase
    Gene namesi
    Name:ampD
    OrganismiCitrobacter freundii
    Taxonomic identifieri546 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeCitrobacterCitrobacter freundii complex

    Subcellular locationi

    Cytoplasm By similarity

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 1871871,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpDPRO_0000164411Add
    BLAST

    Structurei

    Secondary structure

    1
    187
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi11 – 133
    Beta strandi19 – 213
    Helixi23 – 253
    Beta strandi30 – 367
    Helixi47 – 526
    Helixi62 – 676
    Beta strandi75 – 784
    Turni80 – 823
    Beta strandi84 – 863
    Beta strandi92 – 954
    Beta strandi100 – 1023
    Helixi108 – 1114
    Beta strandi112 – 1198
    Beta strandi121 – 1233
    Helixi127 – 14317
    Helixi145 – 1495
    Beta strandi151 – 1533
    Helixi154 – 1574
    Turni159 – 1613
    Turni164 – 1685
    Helixi171 – 1777

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1J3GNMR-A1-187[»]
    2Y28X-ray1.80A/B/C1-187[»]
    2Y2BX-ray1.90A/B/C1-187[»]
    2Y2CX-ray1.80A/B/C1-187[»]
    2Y2DX-ray2.00A/B/C1-187[»]
    2Y2EX-ray2.00A/B/C1-187[»]
    ProteinModelPortaliP82974.
    SMRiP82974. Positions 1-187.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP82974.

    Family & Domainsi

    Sequence similaritiesi

    Family and domain databases

    Gene3Di3.40.80.10. 1 hit.
    InterProiIPR002502. Amidase_domain.
    [Graphical view]
    PfamiPF01510. Amidase_2. 1 hit.
    [Graphical view]
    SMARTiSM00644. Ami_2. 1 hit.
    [Graphical view]
    SUPFAMiSSF55846. SSF55846. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P82974-1 [UniParc]FASTAAdd to Basket

    « Hide

    MLLDEGWLAE ARRVPSPHYD CRPDDENPSL LVVHNISLPP GEFGGPWIDA    50
    LFTGTIDPNA HPYFAGIAHL RVSAHCLIRR DGEIVQYVPF DKRAWHAGVS 100
    SYQGRERCND FSIGIELEGT DTLAYTDAQY QQLAAVTNAL ITRYPAIANN 150
    MTGHCNIAPE RKTDPGPSFD WARFRALVTP SSHKEMT 187
    Length:187
    Mass (Da):20,847
    Last modified:November 2, 2001 - v1
    Checksum:iDE3B49DBA20562AB
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z14002 Genomic DNA. Translation: CAA78390.2.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z14002 Genomic DNA. Translation: CAA78390.2 .

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1J3G NMR - A 1-187 [» ]
    2Y28 X-ray 1.80 A/B/C 1-187 [» ]
    2Y2B X-ray 1.90 A/B/C 1-187 [» ]
    2Y2C X-ray 1.80 A/B/C 1-187 [» ]
    2Y2D X-ray 2.00 A/B/C 1-187 [» ]
    2Y2E X-ray 2.00 A/B/C 1-187 [» ]
    ProteinModelPortali P82974.
    SMRi P82974. Positions 1-187.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Miscellaneous databases

    EvolutionaryTracei P82974.

    Family and domain databases

    Gene3Di 3.40.80.10. 1 hit.
    InterProi IPR002502. Amidase_domain.
    [Graphical view ]
    Pfami PF01510. Amidase_2. 1 hit.
    [Graphical view ]
    SMARTi SM00644. Ami_2. 1 hit.
    [Graphical view ]
    SUPFAMi SSF55846. SSF55846. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Sequences of wild-type and mutant ampD genes of Citrobacter freundii and Enterobacter cloacae."
      Kopp U., Wiedemann B., Lindquist S., Normark S.
      Antimicrob. Agents Chemother. 37:224-228(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: OS60.
    2. "Mutational analysis of the catalytic centre of the Citrobacter freundii AmpD N-acetylmuramyl-L-alanine amidase."
      Genereux C., Dehareng D., Devreese B., Van Beeumen J., Frere J.M., Joris B.
      Biochem. J. 377:111-120(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    3. "NMR structure of Citrobacter freundii AmpD, comparison with bacteriophage T7 lysozyme and homology with PGRP domains."
      Liepinsh E., Genereux C., Dehareng D., Joris B., Otting G.
      J. Mol. Biol. 327:833-842(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR, ZINC-BINDING SITES.

    Entry informationi

    Entry nameiAMPD_CITFR
    AccessioniPrimary (citable) accession number: P82974
    Secondary accession number(s): Q00831
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 2, 2001
    Last sequence update: November 2, 2001
    Last modified: October 1, 2014
    This is version 67 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3