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(-) Description

Title :  CRYSTAL STRUCTURE OF A D-AMINOPEPTIDASE FROM OCHROBACTRUM ANTHROPI
 
Authors :  C. Bompard-Gilles, H. Remaut, V. Villeret, T. Prange, L. Fanuel, J. Joris, J. -M. Frere, J. Van Beeumen
Date :  24 Feb 00  (Deposition) - 04 Oct 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  D-Aminopeptidase, Penicillin Binding Protein, Alpha/Beta Domain, Beta Barrel Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Bompard-Gilles, H. Remaut, V. Villeret, T. Prange, L. Fanuel, M. Delmarcelle, B. Joris, J. Frere, J. Van Beeumen
Crystal Structure Of A D-Aminopeptidase From Ochrobactrum Anthropi, A New Member Of The 'Penicillin-Recognizing Enzyme' Family.
Structure Fold. Des. V. 8 971 2000
PubMed-ID: 10986464  |  Reference-DOI: 10.1016/S0969-2126(00)00188-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-AMINOPEPTIDASE
    Chains: A
    EC Number: 3.4.11.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC18
    Expression System Taxid: 562
    Organism Scientific: OCHROBACTRUM ANTHROPI
    Organism Taxid: 529
    Strain: SCRC C1-38
    Synonym: DAP

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1EI5)

(-) Sites  (0, 0)

(no "Site" information available for 1EI5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EI5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1EI5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EI5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EI5)

(-) Exons   (0, 0)

(no "Exon" information available for 1EI5)

(-) 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:518
 aligned with DAP_OCHAN | Q9ZBA9 from UniProtKB/Swiss-Prot  Length:520

    Alignment length:518
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512        
            DAP_OCHAN     3 KFDTSALEAFVRHIPQNYKGPGGVVAVVKDGEVVLQHAWGFADLRTRTPMTLDTRMPICSVSKQFTCAVLLDAVGEPELLDDALEAYLDKFEDERPAVRDLCNNQSGLRDYWALSVLCGADPEGVFLPAQAQSLLRRLKTTHFEPGSHYSYCNGNFRILADLIEAHTGRTLVDILSERIFAPAGMKRAELISDTALFDECTGYEGDTVRGFLPATNRIQWMGDAGICASLNDMIAWEQFIDATRDDESGLYRRLSGPQTFKDGVAAPYGFGLNLHETGGKRLTGHGGALRGWRCQRWHCADERLSTIAMFNFEGGASEVAFKLMNIALGVSSSEVSRVEADSAWFGSWLDDETGLVLSLEDAGHGRMKARFGTSPEMMDVVSANEARSAVTTIRRDGETIELVRASENLRLSMKRVKGEAKHDIIGRYHSDELDADLLLVSEGGAIYGAFEGFLGKSDMYPLYSVGSDVWLLPVQRSMDAPSPGEWKLVFRRDDKGEITGLSVGCWLARGVEYRRVQP 520
               SCOP domains d1ei5a3 A:3-335 D-aminopeptidase, N-terminal domain                                                                                                                                                                                                                                                                                          d1ei5a1 A:336-417 D-aminopeptidase, middle and C-terminal domains                 d1ei5a2 A:418-520 D-aminopeptidase, middle and C-terminal domains                                       SCOP domains
               CATH domains -------------1ei5A01 A:16-336 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                         1ei5A02 A:337-418  [code=2.40.128.50, no name defined]                            1ei5A03 A:419-520  [code=2.40.128.50, no name defined]                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh...eeeeeeee..eeeeeeeeeeee....ee......ee...hhhhhhhhhhhhhh.hhhhhhhhhhhhh........hhhhhhh......hhhhhhhhh........hhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....ee...hhhh.....eeee...eeee............eeehhhhhhhhhhhhhhh.....hhhhhhh............ee..eeeeee..eeeeeeeeee..eeeeeeee....eeeeeee....hhhhhhhhhhhhhhh...........hhhhheeee......eeeeee....eeeee.....eeeeeee..eee....eeeee..eeeeeehhhheeeeeee..........eeeee....eeeeeeee..eeeeeeee..ee...ee.eeee..eeeeee.........eeeeeeeee.....eeeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ei5 A   3 KFDTSALEAFVRHIPQNYKGPGGVVAVVKDGEVVLQHAWGFADLRTRTPMTLDTRMPICSVSKQFTCAVLLDAVGEPELLDDALEAYLDKFEDERPAVRDLCNNQSGLRDYWALSVLCGADPEGVFLPAQAQSLLRRLKTTHFEPGSHYSYCNGNFRILADLIEAHTGRTLVDILSERIFAPAGMKRAELISDTALFDECTGYEGDTVRGFLPATNRIQWMGDAGICASLNDMIAWEQFIDATRDDESGLYRRLSGPQTFKDGVAAPYGFGLNLHETGGKRLTGHGGALRGWRCQRWHCADERLSTIAMFNFEGGASEVAFKLMNIALGVSSSEVSRVEADSAWFGSWLDDETGLVLSLEDAGHGRMKARFGTSPEMMDVVSANEARSAVTTIRRDGETIELVRASENLRLSMKRVKGEAKHDIIGRYHSDELDADLLLVSEGGAIYGAFEGFLGKSDMYPLYSVGSDVWLLPVQRSMDAPSPGEWKLVFRRDDKGEITGLSVGCWLARGVEYRRVQP 520
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EI5)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (DAP_OCHAN | Q9ZBA9)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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