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* Residue conservation analysis
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PDB id:
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Hydrolase
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Title:
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Complex of the n-acetylmuramyl-l-alanine amidase amid from e the substrate anhydro-n-acetylmuramic acid-l-ala-d-gamma-gl
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Structure:
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N-acetylmuramoyl-l-alanine amidase amid. Chain: a. Engineered: yes. Anhydro-n-acetylmuramic acid-l-ala-d-gamma-glu-l- chain: b. Engineered: yes
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Source:
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Escherichia coli. Organism_taxid: 511145. Strain: k-12 mg1655. Gene: amid, ybjr, b0867, jw0851. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide was chemically synthesized
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Resolution:
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1.75Å
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R-factor:
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0.209
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R-free:
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0.253
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Authors:
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F.Kerff,S.Petrella,R.Herman,E.Sauvage,F.Mercier,A.Luxen,J.M. B.Joris,P.Charlier
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Key ref:
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F.Kerff
et al.
(2010).
Specific Structural Features of the N-Acetylmuramoyl-l-Alanine Amidase AmiD from Escherichia coli and Mechanistic Implications for Enzymes of This Family.
J Mol Biol,
397,
249-259.
PubMed id:
DOI:
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Date:
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09-May-08
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Release date:
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16-Jun-09
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PROCHECK
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Headers
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References
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P75820
(AMID_ECOLI) -
N-acetylmuramoyl-L-alanine amidase AmiD
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Seq:
Struc:
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276 a.a.
257 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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Enzyme class:
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E.C.3.5.1.28
- N-acetylmuramoyl-L-alanine amidase.
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Reaction:
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Hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
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Gene Ontology (GO) functional annotation
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Cellular component
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membrane
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4 terms
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Biological process
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metabolic process
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3 terms
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Biochemical function
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hydrolase activity
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5 terms
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DOI no:
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J Mol Biol
397:249-259
(2010)
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PubMed id:
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Specific Structural Features of the N-Acetylmuramoyl-l-Alanine Amidase AmiD from Escherichia coli and Mechanistic Implications for Enzymes of This Family.
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F.Kerff,
S.Petrella,
F.Mercier,
E.Sauvage,
R.Herman,
A.Pennartz,
A.Zervosen,
A.Luxen,
J.M.Frère,
B.Joris,
P.Charlier.
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ABSTRACT
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AmiD is the fifth identified N-acetylmuramoyl-l-alanine zinc amidase of
Escherichia coli. This periplasmic lipoprotein is anchored in the outer membrane
and has a broad specificity. AmiD is capable of cleaving the intact
peptidoglycan (PG) as well as soluble fragments containing N-acetylmuramic acid
regardless of the presence of an anhydro form or not, unlike the four other
amidases, AmiA, AmiB, AmiC, and AmpD, which have some specificity. AmiD function
is, however, not clearly established but it could be part of the enzymatic
machinery involved in the PG turnover in E. coli. We solved three structures of
the E. coli zinc amidase AmiD devoid of its lipidic anchorage: the holoenzyme,
the apoenzyme in complex with the substrate
anhydro-N-acetylmuramic-acid-l-Ala-gamma-d-Glu-l-Lys, and the holoenzyme in
complex with the l-Ala-gamma-d-Glu-l-Lys peptide, the product of the hydrolysis
of this substrate by AmiD. The AmiD structure shows a relatively flexible
N-terminal extension that allows an easy reach of the PG by the enzyme inserted
into the outer membrane. The C-terminal domain provides a potential extended
geometrical complementarity to the substrate. AmiD shares a common fold with
AmpD, the bacteriophage T7 lysozyme, and the PG recognition proteins, which are
receptor proteins involved in the innate immune responses of a wide range of
organisms. Analysis of the different structures reveals the similarity between
the catalytic mechanism of zinc amidases of the AmiD family and the
thermolysin-related zinc peptidases.
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