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(-) Description

Title :  COMPLEX OF THE N-ACETYLMURAMYL-L-ALANINE AMIDASE AMID FROM E.COLI WITH THE SUBSTRATE ANHYDRO-N-ACETYLMURAMIC ACID-L-ALA-D-GAMMA-GLU-L-LYS
 
Authors :  F. Kerff, S. Petrella, R. Herman, E. Sauvage, F. Mercier, A. Luxen, J. M. B. Joris, P. Charlier
Date :  09 May 08  (Deposition) - 16 Jun 09  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Zinc Amidase, Pgrp, Peptidoglycan Recognizing Protein, Ampd, N- Acetylmuramyl-L-Alanine Amidase, Cell Wall Biogenesis/Degradation, Hydrolase, Lipoprotein, Membrane, Metal-Binding, Outer Membrane, Palmitate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Kerff, S. Petrella, F. Mercier, E. Sauvage, R. Herman, A. Pennartz, A. Zervosen, A. Luxen, J. M. Frere, B. Joris, P. Charlier
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. V. 397 249 2010
PubMed-ID: 20036252  |  Reference-DOI: 10.1016/J.JMB.2009.12.038

(-) Compounds

Molecule 1 - N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID
    Chains: A
    EC Number: 3.5.1.28
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD/MYC-HISA
    Expression System Strain: LMG194
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AMID, YBJR, B0867, JW0851
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 511145
    Strain: K-12 MG1655
 
Molecule 2 - ANHYDRO-N-ACETYLMURAMIC ACID-L-ALA-D-GAMMA-GLU-L-LYS
    Chains: B
    Engineered: YES
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1AH01Mod. Amino Acid2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC ACID
2FGA1Mod. Amino AcidGAMMA-D-GLUTAMIC ACID
3GOL2Ligand/IonGLYCEROL
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1AH01Mod. Amino Acid2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC ACID
2FGA1Mod. Amino AcidGAMMA-D-GLUTAMIC ACID
3GOL2Ligand/IonGLYCEROL
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1AH02Mod. Amino Acid2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC ACID
2FGA2Mod. Amino AcidGAMMA-D-GLUTAMIC ACID
3GOL4Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:18 , ARG A:20 , GLN A:21 , GLN A:74 , LEU A:75 , VAL A:76 , PRO A:77 , HOH A:499BINDING SITE FOR RESIDUE GOL A 262
2AC2SOFTWAREGLN A:169 , ALA A:172 , GLN A:173 , TRP A:179 , ASP A:181 , LYS A:257BINDING SITE FOR RESIDUE GOL A 263

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D2Y)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp A:161 -Pro A:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D2Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D2Y)

(-) Exons   (0, 0)

(no "Exon" information available for 3D2Y)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:257
 aligned with AMID_ECOLI | P75820 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:257
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       
           AMID_ECOLI    20 EKGIVEKEGYQLDTRRQAQAAYPRIKVLVIHYTADDFDSSLATLTDKQVSSHYLVPAVPPRYNGKPRIWQLVPEQELAWHAGISAWRGATRLNDTSIGIELENRGWQKSAGVKYFAPFEPAQIQALIPLAKDIIARYHIKPENVVAHADIAPQRKDDPGPLFPWQQLAQQGIGAWPDAQRVNFYLAGRAPHTPVDTASLLELLARYGYDVKPDMTPREQRRVIMAFQMHFRPTLYNGEADAETQAIAEALLEKYGQD 276
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....eee.............eeeeee...hhhhhhhhhh.......eee.....ee..ee..ee..............ee..ee.hhh.eeeeee....eeee..eeee...hhhhhhhhhhhhhhhhhhhh.hhh.eeehhhhh...........hhhhhhhh......hhhhhhhhhh........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d2y A   5 EKGIVEKEGYQLDTRRQAQAAYPRIKVLVIHYTADDFDSSLATLTDKQVSSHYLVPAVPPRYNGKPRIWQLVPEQELAWHAGISAWRGATRLNDTSIGIELENRGWQKSAGVKYFAPFEPAQIQALIPLAKDIIARYHIKPENVVAHADIAPQRKDDPGPLFPWQQLAQQGIGAWPDAQRVNFYLAGRAPHTPVDTASLLELLARYGYDVKPDMTPREQRRVIMAFQMHFRPTLYNGEADAETQAIAEALLEKYGQD 261
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       


Chain B from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3d2y B   1 xAxK   4
                            | | 
                            1-AH0
                              3-FGA
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3D2Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D2Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D2Y)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (AMID_ECOLI | P75820)
molecular function
    GO:0009392    N-acetyl-anhydromuramoyl-L-alanine amidase activity    Catalysis of the reaction: GlcNAc-1,6-anhMurNAc-L-Ala-gamma-D-Glu-DAP-D-Ala + H2O glcNAc-1,6-anhMurNAc + L-Ala-gamma-D-Glu-DAP-D-Ala.
    GO:0008745    N-acetylmuramoyl-L-alanine amidase activity    Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009253    peptidoglycan catabolic process    The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0009254    peptidoglycan turnover    The continual breakdown and regeneration of peptidoglycan required to maintain the cell wall.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019867    outer membrane    The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

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  3.5.1.28
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        AMID_ECOLI | P75820: 2bh7 2wkx 3d2z

(-) Related Entries Specified in the PDB File

2bgx STRUCTURE OF THE N-ACETYLMURAMYL-L-ALANINE AMIDASE AMID FROM E. COLI
2bh7 SEMET DERIVATIVE OF THE N-ACETYLMURAMYL-L-ALANINE AMIDASE AMID FROM E. COLI
3d2z