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(-) Description

Title :  CRYSTAL STRUCTURE OF PHNP IN COMPLEX WITH ORTHOVANADATE
 
Authors :  K. Podzelinska, Y. M. Kim, D. Zechel, F. Faucher, Z. Jia
Date :  04 Oct 10  (Deposition) - 05 Jan 11  (Release) - 05 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphodiesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Podzelinska, Y. M. Kim, D. Zechel, F. Faucher, Z. Jia
Crystal Structure Of Phnp In Complex With Orthovanadate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN PHNP
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: B4092, JW4053, PHNP
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION
2VO42Ligand/IonVANADATE ION
3ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:78 , ASP B:80 , HIS B:143 , ASP B:164 , HIS B:200 , HIS B:222 , MN B:260 , MN B:261 , HOH B:277 , HOH B:371 , HOH B:407 , HOH B:428BINDING SITE FOR RESIDUE VO4 B 259
2AC2SOFTWAREHIS A:78 , ASP A:80 , HIS A:143 , ASP A:164 , ASN A:199 , HIS A:200 , HIS A:222 , MN A:260 , MN A:261 , HOH A:272 , HOH A:345 , HOH A:376BINDING SITE FOR RESIDUE VO4 A 259
3AC3SOFTWAREHIS A:76 , HIS A:78 , HIS A:143 , ASP A:164 , VO4 A:259 , MN A:261 , HOH A:272BINDING SITE FOR RESIDUE MN A 260
4AC4SOFTWAREASP A:80 , HIS A:81 , ASP A:164 , HIS A:222 , VO4 A:259 , MN A:260 , HOH A:272BINDING SITE FOR RESIDUE MN A 261
5AC5SOFTWAREASP B:80 , HIS B:81 , ASP B:164 , HIS B:222 , VO4 B:259 , MN B:261 , HOH B:277BINDING SITE FOR RESIDUE MN B 260
6AC6SOFTWAREHIS B:76 , HIS B:78 , HIS B:143 , ASP B:164 , VO4 B:259 , MN B:260 , HOH B:277BINDING SITE FOR RESIDUE MN B 261
7AC7SOFTWARECYS A:21 , CYS A:23 , CYS A:26 , HIS A:225BINDING SITE FOR RESIDUE ZN A 262
8AC8SOFTWARECYS B:21 , CYS B:23 , CYS B:26 , HIS B:225BINDING SITE FOR RESIDUE ZN B 262

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P2U)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Val A:16 -Pro A:17
2Ser A:163 -Asp A:164
3Ala A:196 -Pro A:197
4Val B:16 -Pro B:17
5Ser B:163 -Asp B:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P2U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P2U)

(-) Exons   (0, 0)

(no "Exon" information available for 3P2U)

(-) 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:249
 aligned with PHNP_ECOLI | P16692 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
           PHNP_ECOLI     2 SLTLTLTGTGGAQGVPAWGCECAACARARRSPQYRRQPCSGVVKFNDAITLIDAGLHDLADRWSPGSFQQFLLTHYHMDHVQGLFPLRWGVGDPIPVYGPPDEQGCDDLFKHPGLLDFSHTVEPFVVFDLQGLQVTPLPLNHSKLTFGYLLETAHSRVAWLSDTAGLPEKTLKFLRNNQPQVMVMDCSHPPRADAPRNHCDLNTVLALNQVIRSPRVILTHISHQFDAWLMENALPSGFEVGFDGMEIG 250
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.............hhhhhhhhhhhhhh....eeeeee..eeeee.....hhhhhh......eee....hhhhhhhhhhhh......eeeee................eeeeee......eee..eeeeeee.......eeeeee....eeeee......hhhhhhhhhhh...eeeee..............hhhhhhhhhhhhh...eeee..hhhhhhhhh.......eee....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p2u A   2 SLTLTLTGTGGAQGVPAWGCECAACARARRSPQYRRQPCSGVVKFNDAITLIDAGLHDLADRWSPGSFQQFLLTHYHMDHVQGLFPLRWGVGDPIPVYGPPDEQGCDDLFKHPGLLDFSHTVEPFVVFDLQGLQVTPLPLNHSKLTFGYLLETAHSRVAWLSDTAGLPEKTLKFLRNNQPQVMVMDCSHPPRADAPRNHCDLNTVLALNQVIRSPRVILTHISHQFDAWLMENALPSGFEVGFDGMEIG 250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         


Chain B from PDB  Type:PROTEIN  Length:250
 aligned with PHNP_ECOLI | P16692 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
           PHNP_ECOLI     2 SLTLTLTGTGGAQGVPAWGCECAACARARRSPQYRRQPCSGVVKFNDAITLIDAGLHDLADRWSPGSFQQFLLTHYHMDHVQGLFPLRWGVGDPIPVYGPPDEQGCDDLFKHPGLLDFSHTVEPFVVFDLQGLQVTPLPLNHSKLTFGYLLETAHSRVAWLSDTAGLPEKTLKFLRNNQPQVMVMDCSHPPRADAPRNHCDLNTVLALNQVIRSPRVILTHISHQFDAWLMENALPSGFEVGFDGMEIGV 251
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------Lactamase_B_2-3p2uB01 B:30-223                                                                                                                                                                    ---------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------Lactamase_B_2-3p2uB02 B:30-223                                                                                                                                                                    ---------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeee.............hhhhhhhhhhhhhh....eeeeee..eeeee.....hhhhhh......eee....hhhhhhhhhhhh......eeeee................eeeeee......eee..eeeeeee.......eeeeeee..eeeeee......hhhhhhhhhhh...eeeee..............hhhhhhhhhhhhh...eeee..hhhhhhhhh.......eee....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p2u B   2 SLTLTLTGTGGAQGVPAWGCECAACARARRSPQYRRQPCSGVVKFNDAITLIDAGLHDLADRWSPGSFQQFLLTHYHMDHVQGLFPLRWGVGDPIPVYGPPDEQGCDDLFKHPGLLDFSHTVEPFVVFDLQGLQVTPLPLNHSKLTFGYLLETAHSRVAWLSDTAGLPEKTLKFLRNNQPQVMVMDCSHPPRADAPRNHCDLNTVLALNQVIRSPRVILTHISHQFDAWLMENALPSGFEVGFDGMEIGV 251
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
   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 3P2U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P2U)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Metallo-HOrase (67)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PHNP_ECOLI | P16692)
molecular function
    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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
biological process
    GO:0019700    organic phosphonate catabolic process    The chemical reactions and pathways resulting in the breakdown of phosphonates, any organic compound containing one or more C-PO(OH)2 or C-PO(OR)2 (with R=alkyl, aryl) groups. Catabolism of phosphonic acid itself, an inorganic compound without the biochemically relevant C-P bond, is not included.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PHNP_ECOLI | P16692: 3g1p

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