Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

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

Gene

ampD

Organism
Citrobacter freundii
Status
Reviewed-Annotation score: 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

Zn2+Note: Zn2+ is 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

GO - Biological processi

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

GO - Cellular componenti

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 AmpDPRO_0000164411Add
BLAST

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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

        10         20         30         40         50
MLLDEGWLAE ARRVPSPHYD CRPDDENPSL LVVHNISLPP GEFGGPWIDA
60 70 80 90 100
LFTGTIDPNA HPYFAGIAHL RVSAHCLIRR DGEIVQYVPF DKRAWHAGVS
110 120 130 140 150
SYQGRERCND FSIGIELEGT DTLAYTDAQY QQLAAVTNAL ITRYPAIANN
160 170 180
MTGHCNIAPE RKTDPGPSFD WARFRALVTP SSHKEMT
Length:187
Mass (Da):20,847
Last modified:November 2, 2001 - v1
Checksum:iDE3B49DBA20562AB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z14002 Genomic DNA. Translation: CAA78390.2.
RefSeqiWP_003018719.1. NZ_JYFZ01000015.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z14002 Genomic DNA. Translation: CAA78390.2.
RefSeqiWP_003018719.1. NZ_JYFZ01000015.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP82974.

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.
ProtoNetiSearch...

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 22, 2015
This is version 73 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.