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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPONOACETALDEHYDE HYDROLASE COMPLEXED WITH MAGNESIUM AND THE INHIBITOR VINYL SULFONATE
 
Authors :  M. C. Morais, G. Zhang, W. Zhang, D. B. Olsen, D. Dunaway-Mariano, K. N. Allen
Date :  05 Dec 03  (Deposition) - 20 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Schiff-Base Formation; Acid/Base Catalysis; Structural Enzymology; Had Superfamily, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Morais, G. Zhang, W. Zhang, D. B. Olsen, D. Dunaway-Mariano, K. N. Allen
X-Ray Crystallographic And Site-Directed Mutagenesis Analysis Of The Mechanism Of Schiff-Base Formation In Phosphonoacetaldehyde Hydrolase Catalysis
J. Biol. Chem. V. 279 9353 2004
PubMed-ID: 14670958  |  Reference-DOI: 10.1074/JBC.M312345200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHONOACETALDEHYDE HYDROLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK223-3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 1396
    Synonym: PHOSPHONATASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2VSO1Ligand/IonVINYLSULPHONIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:12 , ALA A:14 , ASP A:186BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREASP B:12 , ALA B:14 , ASP B:186 , VSO B:600 , HOH B:616BINDING SITE FOR RESIDUE MG B 502
3AC3SOFTWAREASP B:12 , TRP B:13 , ALA B:14 , GLY B:50 , THR B:126 , GLY B:127 , TYR B:128 , ARG B:160 , MG B:502 , HOH B:616BINDING SITE FOR RESIDUE VSO B 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Arg A:160 -Pro A:161
2Tyr A:176 -Pro A:177
3Arg B:160 -Pro B:161
4Tyr B:176 -Pro B:177

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1RQL)

(-) 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:257
 aligned with PHNX_BACCE | O31156 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:257
                                    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       
           PHNX_BACCE     2 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIEK 258
               SCOP domains d1rqla_ A: Phosphonoacetaldehyde hydrolase                                                                                                                                                                                                                        SCOP domains
               CATH domains 1rqlA01            1rqlA02 A:24-101 Putative phosphatase; domain 2                               1rqlA01 A:5-23,A:102-260  [code=3.40.50.1000, no name defined]                                                                                                 - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...........hhhhhhhhhhhhh.....hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh........hhhhh......hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh..eeeee.........hhhhhhh.hhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rql A   5 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIEK 261
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       


Chain B from PDB  Type:PROTEIN  Length:257
 aligned with PHNX_BACCE | O31156 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:257
                                    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       
           PHNX_BACCE     2 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIEK 258
               SCOP domains d1rqlb_ B: Phosphonoacetaldehyde hydrolase                                                                                                                                                                                                                        SCOP domains
               CATH domains 1rqlB01            1rqlB02 B:24-101 Putative phosphatase; domain 2                               1rqlB01 B:5-23,B:102-260  [code=3.40.50.1000, no name defined]                                                                                                 - CATH domains
           Pfam domains (1) ----HAD_2-1rqlB01 B:9-204                                                                                                                                                                               --------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----HAD_2-1rqlB02 B:9-204                                                                                                                                                                               --------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeee............hhhhhhhhhhh.....hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh........hhhhh......hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhh.eeeee.........hhhhhhh.hhhhhhhhhhhhhhhhhhh...eee....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rql B   5 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIEK 261
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254
   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, 2)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PHNX_BACCE | O31156)
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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0050194    phosphonoacetaldehyde hydrolase activity    Catalysis of the reaction: H(2)O + phosphonoacetaldehyde = acetaldehyde + 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.
    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
        PHNX_BACCE | O31156: 1fez 1rdf 1rqn 1swv 1sww 2iof 2ioh

(-) Related Entries Specified in the PDB File

1fez PHOSPHONOACETALDEHYDE HYDROLASE COMPLEXED WITH MAGNESIUM AND TUNGSTATE
1rqn