P82974 (AMPD_CITFR) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:

ampD

Organism

Citrobacter freundii

Taxonomic identifier

546 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Citrobacter

Protein attributes

Sequence length	187 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.2
Catalytic activity	Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides.
Cofactor	Zinc; required for amidase activity.
Subcellular location	Cytoplasm By similarity.
Sequence similarities	Belongs to the N-acetylmuramoyl-L-alanine amidase 2 family.

Ontologies

Keywords
Biological process	Cell wall biogenesis/degradation
Cellular component	Cytoplasm
Ligand	Metal-binding Zinc
Molecular function	Hydrolase
Technical term	3D-structure
Gene Ontology (GO)
Biological_process	peptidoglycan catabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	N-acetylmuramoyl-L-alanine amidase activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 187

187

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

PRO_0000164411

Sites

Active site

116

1

Proton acceptor By similarity

Metal binding

34

1

Zinc; catalytic

Metal binding

154

1

Zinc; catalytic

Metal binding

164

1

Zinc; catalytic

Site

162

1

Transition state stabilizer By similarity

Secondary structure

1

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187

Helix Strand Turn

Details...

Beta strand

11 – 13

3

Beta strand

19 – 21

3

Helix

23 – 25

3

Beta strand

30 – 36

7

Helix

47 – 52

6

Helix

62 – 67

6

Beta strand

75 – 78

4

Turn

80 – 82

3

Beta strand

84 – 86

3

Beta strand

92 – 95

4

Beta strand

100 – 102

3

Helix

108 – 111

4

Beta strand

112 – 119

8

Beta strand

121 – 123

3

Helix

127 – 143

17

Helix

145 – 149

5

Beta strand

151 – 153

3

Helix

154 – 157

4

Turn

159 – 161

3

Turn

164 – 168

5

Helix

171 – 177

7

Sequences

	Sequence		Length	Mass (Da)
	P82974 [UniParc]. Last modified November 2, 2001. Version 1. Checksum: DE3B49DBA20562AB	FASTA	187	20,847
	10 20 30 40 50 60 MLLDEGWLAE ARRVPSPHYD CRPDDENPSL LVVHNISLPP GEFGGPWIDA LFTGTIDPNA 70 80 90 100 110 120 HPYFAGIAHL RVSAHCLIRR DGEIVQYVPF DKRAWHAGVS SYQGRERCND FSIGIELEGT 130 140 150 160 170 180 DTLAYTDAQY QQLAAVTNAL ITRYPAIANN MTGHCNIAPE RKTDPGPSFD WARFRALVTP SSHKEMT

References

[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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z14002 Genomic DNA. Translation: CAA78390.2.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P82974.

SMR

P82974. Positions 1-187.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

3.40.80.10. 1 hit.

InterPro

IPR002502. Amidase_domain.
[Graphical view]

Pfam

PF01510. Amidase_2. 1 hit.
[Graphical view]

SMART

SM00644. Ami_2. 1 hit.
[Graphical view]

SUPFAM

SSF55846. Amidase_2. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P82974.

Entry information

Entry name

AMPD_CITFR

Accession

Primary (citable) accession number: P82974
Secondary accession number(s): Q00831

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 2, 2001
Last sequence update:	November 2, 2001
Last modified:	April 3, 2013
This is version 63 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program