AMPD_CITFR
ID AMPD_CITFR Reviewed; 187 AA.
AC P82974; Q00831;
DT 02-NOV-2001, integrated into UniProtKB/Swiss-Prot.
DT 02-NOV-2001, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD {ECO:0000305};
DE EC=3.5.1.28 {ECO:0000269|PubMed:14507260};
DE AltName: Full=N-acetylmuramoyl-L-alanine amidase {ECO:0000305};
GN Name=ampD {ECO:0000303|PubMed:8383940};
OS Citrobacter freundii.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
OX NCBI_TaxID=546;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RC STRAIN=OS60;
RX PubMed=8383940; DOI=10.1128/aac.37.2.224;
RA Kopp U., Wiedemann B., Lindquist S., Normark S.;
RT "Sequences of wild-type and mutant ampD genes of Citrobacter freundii and
RT Enterobacter cloacae.";
RL Antimicrob. Agents Chemother. 37:224-228(1993).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION, AND
RP MUTAGENESIS OF HIS-34; TYR-63; GLU-116; HIS-154; LYS-162 AND ASP-164.
RX PubMed=14507260; DOI=10.1042/bj20030862;
RA Genereux C., Dehareng D., Devreese B., Van Beeumen J., Frere J.M.,
RA Joris B.;
RT "Mutational analysis of the catalytic centre of the Citrobacter freundii
RT AmpD N-acetylmuramyl-L-alanine amidase.";
RL Biochem. J. 377:111-120(2004).
RN [3]
RP STRUCTURE BY NMR, ZINC-BINDING SITES, AND COFACTOR.
RX PubMed=12654266; DOI=10.1016/s0022-2836(03)00185-2;
RA Liepinsh E., Genereux C., Dehareng D., Joris B., Otting G.;
RT "NMR structure of Citrobacter freundii AmpD, comparison with bacteriophage
RT T7 lysozyme and homology with PGRP domains.";
RL J. Mol. Biol. 327:833-842(2003).
CC -!- FUNCTION: Involved in cell wall peptidoglycan recycling
CC (PubMed:14507260). Specifically cleaves the amide bond between the
CC lactyl group of N-acetylmuramic acid and the alpha-amino group of the
CC L-alanine in degradation products containing an anhydro N-acetylmuramyl
CC moiety (PubMed:14507260). Is also involved in beta-lactamase induction
CC (PubMed:8383940). {ECO:0000269|PubMed:14507260,
CC ECO:0000269|PubMed:8383940}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolyzes the link between N-acetylmuramoyl residues and L-
CC amino acid residues in certain cell-wall glycopeptides.; EC=3.5.1.28;
CC Evidence={ECO:0000269|PubMed:14507260};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:12654266, ECO:0000269|PubMed:14507260};
CC Note=Zn(2+) is required for amidase activity.
CC {ECO:0000269|PubMed:14507260};
CC -!- ACTIVITY REGULATION: Amidase activity is inhibited by metal chelators
CC such as EDTA, dipicolinic acid or 1,10-phenanthroline.
CC {ECO:0000269|PubMed:14507260}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the N-acetylmuramoyl-L-alanine amidase 2 family.
CC {ECO:0000305}.
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DR EMBL; Z14002; CAA78390.2; -; Genomic_DNA.
DR RefSeq; WP_003018719.1; NZ_VTEC01000028.1.
DR PDB; 1J3G; NMR; -; A=1-187.
DR PDB; 2Y28; X-ray; 1.80 A; A/B/C=1-187.
DR PDB; 2Y2B; X-ray; 1.90 A; A/B/C=1-187.
DR PDB; 2Y2C; X-ray; 1.80 A; A/B/C=1-187.
DR PDB; 2Y2D; X-ray; 2.00 A; A/B/C=1-187.
DR PDB; 2Y2E; X-ray; 2.00 A; A/B/C=1-187.
DR PDBsum; 1J3G; -.
DR PDBsum; 2Y28; -.
DR PDBsum; 2Y2B; -.
DR PDBsum; 2Y2C; -.
DR PDBsum; 2Y2D; -.
DR PDBsum; 2Y2E; -.
DR AlphaFoldDB; P82974; -.
DR BMRB; P82974; -.
DR SMR; P82974; -.
DR STRING; 1333848.CFNIH1_10245; -.
DR OrthoDB; 1584918at2; -.
DR EvolutionaryTrace; P82974; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008745; F:N-acetylmuramoyl-L-alanine amidase activity; IDA:CACAO.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0009253; P:peptidoglycan catabolic process; IEA:InterPro.
DR CDD; cd06583; PGRP; 1.
DR Gene3D; 3.40.80.10; -; 1.
DR InterPro; IPR036505; Amidase/PGRP_sf.
DR InterPro; IPR002502; Amidase_domain.
DR Pfam; PF01510; Amidase_2; 1.
DR SMART; SM00644; Ami_2; 1.
DR SUPFAM; SSF55846; SSF55846; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell wall biogenesis/degradation; Cytoplasm; Hydrolase;
KW Metal-binding; Zinc.
FT CHAIN 1..187
FT /note="1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD"
FT /id="PRO_0000164411"
FT DOMAIN 30..167
FT /note="N-acetylmuramoyl-L-alanine amidase"
FT /evidence="ECO:0000255"
FT ACT_SITE 116
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P75820"
FT BINDING 34
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:12654266"
FT BINDING 154
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:12654266"
FT BINDING 164
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:12654266"
FT SITE 162
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P75820"
FT MUTAGEN 34
FT /note="H->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:14507260"
FT MUTAGEN 63
FT /note="Y->F: 6-fold decrease in activity."
FT /evidence="ECO:0000269|PubMed:14507260"
FT MUTAGEN 116
FT /note="E->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:14507260"
FT MUTAGEN 154
FT /note="H->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:14507260"
FT MUTAGEN 154
FT /note="H->N: Retains both its capacity to bind the zinc ion
FT and good amidase activity."
FT /evidence="ECO:0000269|PubMed:14507260"
FT MUTAGEN 162
FT /note="K->H,Q: Almost loss of activity."
FT /evidence="ECO:0000269|PubMed:14507260"
FT MUTAGEN 164
FT /note="D->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:14507260"
FT STRAND 11..13
FT /evidence="ECO:0007829|PDB:2Y28"
FT STRAND 19..21
FT /evidence="ECO:0007829|PDB:2Y28"
FT HELIX 23..25
FT /evidence="ECO:0007829|PDB:2Y28"
FT STRAND 30..36
FT /evidence="ECO:0007829|PDB:2Y28"
FT HELIX 47..52
FT /evidence="ECO:0007829|PDB:2Y28"
FT HELIX 62..67
FT /evidence="ECO:0007829|PDB:2Y28"
FT STRAND 75..78
FT /evidence="ECO:0007829|PDB:2Y28"
FT TURN 80..82
FT /evidence="ECO:0007829|PDB:1J3G"
FT STRAND 84..86
FT /evidence="ECO:0007829|PDB:2Y28"
FT STRAND 92..95
FT /evidence="ECO:0007829|PDB:2Y28"
FT STRAND 100..102
FT /evidence="ECO:0007829|PDB:1J3G"
FT HELIX 108..111
FT /evidence="ECO:0007829|PDB:2Y28"
FT STRAND 112..119
FT /evidence="ECO:0007829|PDB:2Y28"
FT STRAND 121..123
FT /evidence="ECO:0007829|PDB:2Y28"
FT HELIX 127..143
FT /evidence="ECO:0007829|PDB:2Y28"
FT HELIX 145..149
FT /evidence="ECO:0007829|PDB:2Y28"
FT STRAND 151..153
FT /evidence="ECO:0007829|PDB:2Y28"
FT HELIX 154..157
FT /evidence="ECO:0007829|PDB:2Y28"
FT TURN 159..161
FT /evidence="ECO:0007829|PDB:2Y28"
FT TURN 164..168
FT /evidence="ECO:0007829|PDB:2Y2D"
FT HELIX 171..177
FT /evidence="ECO:0007829|PDB:2Y28"
SQ SEQUENCE 187 AA; 20847 MW; DE3B49DBA20562AB CRC64;
MLLDEGWLAE ARRVPSPHYD CRPDDENPSL LVVHNISLPP GEFGGPWIDA LFTGTIDPNA
HPYFAGIAHL RVSAHCLIRR DGEIVQYVPF DKRAWHAGVS SYQGRERCND FSIGIELEGT
DTLAYTDAQY QQLAAVTNAL ITRYPAIANN MTGHCNIAPE RKTDPGPSFD WARFRALVTP
SSHKEMT
