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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHONOACETATE HYDROLASE FROM SINORHIZOBIUM MELILOTI 1021 IN COMPLEX WITH PHOSPHONOACETATE
 
Authors :  V. Agarwal, S. K. Nair
Date :  19 Jul 11  (Deposition) - 03 Aug 11  (Release) - 09 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Alkaline Phosphatase Superfamily, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Agarwal, S. A. Borisova, W. W. Metcalf, W. A. Van Der Donk, S. K. Nai
Structural And Mechanistic Insights Into C-P Bond Hydrolysi By Phosphonoacetate Hydrolase.
Chem. Biol. V. 18 1230 2011
PubMed-ID: 22035792  |  Reference-DOI: 10.1016/J.CHEMBIOL.2011.07.019

(-) Compounds

Molecule 1 - PHOSPHONOACETATE HYDROLASE
    Chains: A
    EC Number: 3.6.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PHNA, RB0978, SM_B21538
    Mutation: YES
    Organism Common: ENSIFER MELILOTI
    Organism Scientific: SINORHIZOBIUM MELILOTI
    Organism Taxid: 266834
    Strain: 1021

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1PAE1Ligand/IonPHOSPHONOACETIC ACID
2ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:29 , ALA A:68 , ASP A:211 , ASP A:250 , HIS A:251 , PAE A:503BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREASP A:211 , HIS A:215 , HIS A:377 , PAE A:503BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWAREASP A:29 , PHE A:67 , ALA A:68 , ASP A:211 , HIS A:215 , HIS A:251 , HIS A:377 , HOH A:457 , HOH A:481 , ZN A:501 , ZN A:502 , HOH A:684BINDING SITE FOR RESIDUE PAE A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T02)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:64 -Pro A:65
2Ala A:399 -Pro A:400

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T02)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T02)

(-) Exons   (0, 0)

(no "Exon" information available for 3T02)

(-) 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:413
 aligned with Q92UV8_RHIME | Q92UV8 from UniProtKB/TrEMBL  Length:424

    Alignment length:413
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413   
         Q92UV8_RHIME     4 MSKISVTVNGRRYPWPRVPAIAVCLDGCEPAYLDAAIDAGLMPALKRIKERGAVRLAHSVIPSFTNPNNLSIATGSPPAVHGICGNYLYEPSTGEEVMMNDPKFLRAPTIFQAFYDAGARVAVVTAKDKLRALLGKGLRFDEGRAVCFSSEKSDKATRAEHGIDNASAWLGRPVPEVYSAALSEFVFAAGVKLLREFRPDIMYLTTTDYVQHKYAPGVPEANSFYEMFDRYLAELDGLGAAIVVTADHGMKPKHKADGSPDVIYVQDLLDEWLGKDAARVILPITDPYVVHHGALGSFATAYLPDGCDRSEIMARLKAIQGVDVVLGREEACRRFELPEDRIGDIVLVSSENKTLGTSEHRHDLAALDEPLRSHGGLTEQEVPFIVNRVLPELPNAPRLRNFDAFFYAVTAAA 416
               SCOP domains d3t02a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeee....hhhhhhhhhhh..hhhhhhhhhhheeeeee.....hhhhhhhhhhhh.hhhhhh....eeee....eeee..hhhhh...hhhhhhhhh...eeeee.hhhhhhhhh.........eeeee..hhhhhhhhhhh..hhhhhhh.......hhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeee.....ee.........eeehhhhhhhhhh....eee................eeeee.....hhhhhhhhhhh...eeeeeehhhhhhhhh.hhhhh..eeeee....eee...............ee..hhhh.eeeeee.............hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t02 A   4 MSKISVTVNGRRYPWPRVPAIAVCLDGCEPAYLDAAIDAGLMPALKRIKERGAVRLAHSVIPSFANPNNLSIATGSPPAVHGICGNYLYEPSTGEEVMMNDPKFLRAPTIFQAFYDAGARVAVVTAKDKLRALLGKGLRFDEGRAVCFSSEKSDKATRAEHGIDNASAWLGRPVPEVYSAALSEFVFAAGVKLLREFRPDIMYLTTTDYVQHKYAPGVPEANSFYEMFDRYLAELDGLGAAIVVTADHGMKPKHKADGSPDVIYVQDLLDEWLGKDAARVILPITDPYVVHHGALGSFATAYLPDGCDRSEIMARLKAIQGVDVVLGREEACRRFELPEDRIGDIVLVSSENKTLGTSEHRHDLAALDEPLRSHGGLTEQEVPFIVNRVLPELPNAPRLRNFDAFFYAVTAAA 416
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T02)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T02)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q92UV8_RHIME | Q92UV8)
molecular function
    GO:0035529    NADH pyrophosphatase activity    Catalysis of the reaction: NADH + H2O = AMP + NMNH + 2 H+.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0004551    nucleotide diphosphatase activity    Catalysis of the reaction: a dinucleotide + H2O = 2 mononucleotides.
    GO:0047400    phosphonoacetate hydrolase activity    Catalysis of the reaction: H(2)O + phosphonoacetate = acetate + H(+) + phosphate.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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 Related Entries

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

UniProtKB/TrEMBL
        Q92UV8_RHIME | Q92UV8: 3szy 3szz 3t00 3t01

(-) Related Entries Specified in the PDB File

3szy CRYSTAL STRUCTURE OF PHOSPHONOACETATE HYDROLASE FROM SINORHIZOBIUM MELILOTI 1021 IN APO FORM
3szz CRYSTAL STRUCTURE OF PHOSPHONOACETATE HYDROLASE FROM SINORHIZOBIUM MELILOTI 1021 IN COMPLEX WITH ACETATE
3t00 CRYSTAL STRUCTURE OF PHOSPHONOACETATE HYDROLASE FROM SINORHIZOBIUM MELILOTI 1021 IN COMPLEX WITH VANADATE
3t01 CRYSTAL STRUCTURE OF PHOSPHONOACETATE HYDROLASE FROM SINORHIZOBIUM MELILOTI 1021 IN COMPLEX WITH PHOSPHONOFORMATE