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P82974

- AMPD_CITFR

UniProt

P82974 - AMPD_CITFR

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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

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 acceptor By similarity
Metal bindingi154 – 1541Zinc; catalytic
Sitei162 – 1621Transition state stabilizer By similarity
Metal bindingi164 – 1641Zinc; catalytic

GO - Molecular functioni

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

GO - Biological processi

  1. peptidoglycan catabolic process Source: InterPro
Complete GO annotation...

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
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 1871871,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD
PRO_0000164411Add
BLAST

Structurei

Secondary structure

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.

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: July 9, 2014
This is version 66 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

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