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Title :  DIFFERENT MODES OF VANCOMYCIN AND D-ALANYL-D-ALANINE PEPTIDASE BINDING TO CELL WALL PEPTIDE AND A POSSIBLE ROLE FOR THE VANCOMYCIN RESISTANCE PROTEIN
 
Authors :  J. R. Knox
Date :  16 Nov 90  (Deposition) - 31 Jan 94  (Release) - 31 Jan 94  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  E,P
Keywords :  Hydrolase(Transpeptidase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Knox, R. F. Pratt
Different Modes Of Vancomycin And D-Alanyl-D-Alanine Peptidase Binding To Cell Wall Peptide And A Possible Role For The Vancomycin Resistance Protein.
Antimicrob. Agents Chemother. V. 34 1342 1990
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
    Chains: E
    EC Number: 3.4.16.4
    Engineered: YES
 
Molecule 2 - 
    Chains: P
    Engineered: YES

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2PTE)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Theoretical Model
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain E from PDB  Type:PROTEIN  Length:28
 aligned with DAC_STRSR | P15555 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:242
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331  
            DAC_STRSR    92 GSVTKSFSAVVLLQLVDEGKLDLDASVNTYLPGLLPDDRITVRQVMSHRSGLYDYTNDMFAQTVPGFESVRNKVFSYQDLITLSLKHGVTNAPGAAYSYSNTNFVVAGMLIEKLTGHSVATEYQNRIFTPLNLTDTFYVHPDTVIPGTHANGYLTPDEAGGALVDSTEQTVSWAQSAGAVISSTQDLDTFFSALMSGQLMSAAQLAQMQQWTTVNSTQGYGLGLRRRDLSCGISVYGHTGTV 333
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh----------------------------..---------------------------------------------------------------......-----------------------------------------------------------.....--------------------------------------------------.....--------------..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pte E  61 GSVTK----------------------------LL---------------------------------------------------------------YSNTNF-----------------------------------------------------------VDSTE--------------------------------------------------GYGLG--------------HTGTV 302
                                |    -         -         -   ||    -         -         -         -         -         -       160   |     -         -         -         -         -         -   |   | -         -         -         -         -       280  |      -       300  
                               65                           94|                                                             159  164                                                         224 228                                                279 283            298    
                                                             95                                                                                                                                                                                                               


Chain P from PDB  Type:PROTEIN  Length:3
                                   
               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
                 2pte P   1 KAA   3
   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 2PTE)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PTE)

(-) Gene Ontology  (9, 9)

Theoretical Model(hide GO term definitions)
Chain E   (DAC_STRSR | P15555)
molecular function
    GO:0004180    carboxypeptidase activity    Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0009002    serine-type D-Ala-D-Ala carboxypeptidase activity    Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
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:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DAC_STRSR | P15555: 1cef 1ceg 1hvb 1ikg 1iki 1mpl 1pw1 1pw8 1pwc 1pwd 1pwg 1scw 1sde 1yqs 3pte

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