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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 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. cell wall organization Source: UniProtKB-KW
  2. 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-KW
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 – 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

        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:
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 29, 2014
This is version 68 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