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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PROBABLE DIPEPTIDASE PVDM FROM PSEUDOMONAS AERUGINOSA
 
Authors :  J. B. Bonanno, Y. Patskovsky, M. Dickey, K. T. Bain, M. Mendoza, R. Fong, D. Smith, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  23 Oct 07  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Hydrolase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Bonanno, Y. Patskovsky, M. Dickey, K. T. Bain, M. Mendoza, R. Fong, D. Smith, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of The Probable Dipeptidase Pvdm From Pseudomonas Aeruginosa.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE DIPEPTIDASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 34-448
    Gene: PVDM, PA2393
    Mutation: YES
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: PVDM

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CD2Ligand/IonCADMIUM ION
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:48 , GLU A:51 , GLU A:231 , ASP A:235BINDING SITE FOR RESIDUE CD A 1
2AC2SOFTWAREHIS A:384 , HOH A:530 , HOH A:792 , HOH A:793 , HOH A:794BINDING SITE FOR RESIDUE CD A 2
3AC3SOFTWAREGLU A:349BINDING SITE FOR RESIDUE MG A 449
4AC4SOFTWAREHIS A:45 , ASP A:420 , HOH A:795BINDING SITE FOR RESIDUE CA A 450
5AC5SOFTWAREASP A:120 , HIS A:124BINDING SITE FOR RESIDUE CA A 451

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B40)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3B40)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B40)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B40)

(-) Exons   (0, 0)

(no "Exon" information available for 3B40)

(-) Sequences/Alignments

Asymmetric/Biological 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:400
 aligned with Q5DIQ1_PSEAI | Q5DIQ1 from UniProtKB/TrEMBL  Length:448

    Alignment length:405
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437     
         Q5DIQ1_PSEAI    38 YPRKVMQHAEELHERILSFDSRITVPLDFGTTGNEVDKDGPGQLDLVKAGRGRLSGAALAIFGWPEMWNGPNAPHKPTPGFVDEARHQQEIRYKILTGMVRDFPNQVGIAYSPEDFRRLAMEGKFAIVMSMLNAYPLGDDLSQLDKWAARGVRMFGFSYVGNNDWADSSRPLPFFNDSPDALGGLSPLGKQAVERLNDLGVIIDVSQMSTKALEQVAALSRAPIVASHSAPRALVDIKRNLSDHEMQLIKDSGGVIQVVGFPAYLRPLSKPTLDKLDALRARFDLPPLEGLDYALMPGDPIITIWPEQRFGEYASALYGILEEEPKAGLKELVDAIDYTVKKVGIDHVGISSDFNDGGGVDGWKDVSEIRNVTAELITRGYSDADIAKLWGGNFLRAWGEVQKRA 442
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b40A01 A:38-304,A:363-442 Metal-dependent hydrolases                                                                                                                                                                                                                      3b40A02 A:305-362 Helix hairpin bin                       3b40A01 A:38-304,A:363-442 Metal-dependent hydrolases                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....eeeee.....................hhhhhhhhh..eeeeeee......-----......hhhhhhhhhhhhhhhhhhhhhhhh...eee..hhhhhhhhhhh..eeeeeeee.hhhhh..hhhhhhhhhh...eee...............hhhhh.........hhhhhhhhhhhhhhh.eee....hhhhhhhhhhhh...eeeeee............hhhhhhhhhhh..eeeee.hhhhhh..hhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b40 A  38 YPRKVMQHAEELHERILSFDSRITVPLDFGTTGNEVDKDGPGQLDLVKAGRGRLSGAALAIFGWPEMW-----PHKPTPGFVDEARHQQEIRYKILTGMVRDFPNQVGIAYSPEDFRRLAMEGKFAIVMSMLNAYPLGDDLSQLDKWAARGVRMFGFSYVGNNDWADSSRPLPFFNDSPDALGGLSPLGKQAVERLNDLGVIIDVSQMSTKALEQVAALSRAPIVASHSAPRALVDIKRNLSDHEMQLIKDSGGVIQVVGFPAYLRPLSKPTLDKLDALRARFDLPPLEGLDYALMPGDPIITIWPEQRFGEYASALYGILEEEPKAGLKELVDAIDYTVKKVGIDHVGISSDFNDGGGVDGWKDVSEIRNVTAELITRGYSDADIAKLWGGNFLRAWGEVQKRA 442
                                    47        57        67        77        87        97       | -   |   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437     
                                                                                             105   111                                                                                                                                                                                                                                                                                                                                           


Chain A from PDB  Type:PROTEIN  Length:400
 aligned with Q9I187_PSEAE | Q9I187 from UniProtKB/TrEMBL  Length:448

    Alignment length:405
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437     
         Q9I187_PSEAE    38 YPRKVMKHAEELHERILSFDSRITIPPDFGTEGNEFDKDGPNQLDLVKAGRGRLSGAALAIFGWPEMWNGPNAPHKPTPGFVDEARHQQEIRYKILTGMVRDFPNQVGIAYSPEDFRRLAMEGKFAIVMSMLNAYPLGDDLSQLDKWAARGVRMFGFNYVGNNDWSDSSRPLPFFNDTADALGGLSPLGKQAVERLNDLGVIIDVSQMSTKALEQVAALSRAPIVASHSAPRALVDIKRNLSDHEMQLIKDSGGVIQVVGFPAYLRPLSKPTLDKLNALRARFDLPPLEGLDYALMPGDPIITIWPEQRFGEYASALYGILEEEPKAGLKELVDAIDYTVKKVGIDHVGISSDFNDGGGVDGWKDVSEIRNVTAELITRGYSDADIAKLWGGNFLRAWGEVQKRA 442
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b40A01 A:38-304,A:363-442 Metal-dependent hydrolases                                                                                                                                                                                                                      3b40A02 A:305-362 Helix hairpin bin                       3b40A01 A:38-304,A:363-442 Metal-dependent hydrolases                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....eeeee.....................hhhhhhhhh..eeeeeee......-----......hhhhhhhhhhhhhhhhhhhhhhhh...eee..hhhhhhhhhhh..eeeeeeee.hhhhh..hhhhhhhhhh...eee...............hhhhh.........hhhhhhhhhhhhhhh.eee....hhhhhhhhhhhh...eeeeee............hhhhhhhhhhh..eeeee.hhhhhh..hhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b40 A  38 YPRKVMQHAEELHERILSFDSRITVPLDFGTTGNEVDKDGPGQLDLVKAGRGRLSGAALAIFGWPEMW-----PHKPTPGFVDEARHQQEIRYKILTGMVRDFPNQVGIAYSPEDFRRLAMEGKFAIVMSMLNAYPLGDDLSQLDKWAARGVRMFGFSYVGNNDWADSSRPLPFFNDSPDALGGLSPLGKQAVERLNDLGVIIDVSQMSTKALEQVAALSRAPIVASHSAPRALVDIKRNLSDHEMQLIKDSGGVIQVVGFPAYLRPLSKPTLDKLDALRARFDLPPLEGLDYALMPGDPIITIWPEQRFGEYASALYGILEEEPKAGLKELVDAIDYTVKKVGIDHVGISSDFNDGGGVDGWKDVSEIRNVTAELITRGYSDADIAKLWGGNFLRAWGEVQKRA 442
                                    47        57        67        77        87        97       | -   |   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437     
                                                                                             105   111
   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 3B40)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B40)

(-) Gene Ontology  (3, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5DIQ1_PSEAI | Q5DIQ1)
molecular function
    GO:0016805    dipeptidase activity    Catalysis of the hydrolysis of a dipeptide.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Chain A   (Q9I187_PSEAE | Q9I187)
molecular function
    GO:0016805    dipeptidase activity    Catalysis of the hydrolysis of a dipeptide.
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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