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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)DescriptionActionsGraphical viewLength
Metal bindingi34Zinc; catalytic1
Active sitei116Proton acceptorBy similarity1
Metal bindingi154Zinc; catalytic1
Sitei162Transition state stabilizerBy similarity1
Metal bindingi164Zinc; catalytic1

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeCitrobacterCitrobacter freundii complex

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001644111 – 1871,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpDAdd BLAST187

Structurei

Secondary structure

1187
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi11 – 13Combined sources3
Beta strandi19 – 21Combined sources3
Helixi23 – 25Combined sources3
Beta strandi30 – 36Combined sources7
Helixi47 – 52Combined sources6
Helixi62 – 67Combined sources6
Beta strandi75 – 78Combined sources4
Turni80 – 82Combined sources3
Beta strandi84 – 86Combined sources3
Beta strandi92 – 95Combined sources4
Beta strandi100 – 102Combined sources3
Helixi108 – 111Combined sources4
Beta strandi112 – 119Combined sources8
Beta strandi121 – 123Combined sources3
Helixi127 – 143Combined sources17
Helixi145 – 149Combined sources5
Beta strandi151 – 153Combined sources3
Helixi154 – 157Combined sources4
Turni159 – 161Combined sources3
Turni164 – 168Combined sources5
Helixi171 – 177Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP82974.

Family & Domainsi

Sequence similaritiesi

Family and domain databases

CDDicd06583. PGRP. 1 hit.
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_LLJR01000002.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z14002 Genomic DNA. Translation: CAA78390.2.
RefSeqiWP_003018719.1. NZ_LLJR01000002.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP82974.

Family and domain databases

CDDicd06583. PGRP. 1 hit.
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...

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: November 2, 2016
This is version 80 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

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 one 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.