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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHONOACETALDEHYDE HYDROLASE WITH SODIUM BOROHYDRIDE-REDUCED SUBSTRATE INTERMEDIATE
 
Authors :  K. A. Allen, S. D. Lahiri, G. Zhang, D. Dunaway-Mariano
Date :  10 Oct 06  (Deposition) - 17 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,K
Keywords :  Phosphonoacetaldehyde Hydrolase, Haloacid Dehalogenase Superfamily (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. D. Lahiri, G. Zhang, D. Dunaway-Mariano, K. N. Allen
Diversification Of Function In The Haloacid Dehalogenase Enzyme Superfamily: The Role Of The Cap Domain In Hydrolytic Phosphoruscarbon Bond Cleavage.
Bioorg. Chem. V. 34 394 2006
PubMed-ID: 17070898  |  Reference-DOI: 10.1016/J.BIOORG.2006.09.007
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHONOACETALDEHYDE HYDROLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 1396
 
Molecule 2 - PHOSPHONOACETALDEHYDE HYDROLASE
    Chains: K
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 1396

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AK

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1LDH1Mod. Amino AcidN~6~-ETHYL-L-LYSINE
2MG2Ligand/IonMAGNESIUM ION
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:12 , ALA A:14 , GLY A:50 , LYS A:53 , THR A:126 , GLY A:127 , MG A:462BINDING SITE FOR RESIDUE PO4 A 361
2AC2SOFTWAREASP A:12 , ALA A:14 , ASP A:186 , PO4 A:361BINDING SITE FOR RESIDUE MG A 462
3AC3SOFTWAREASP K:12 , TRP K:13 , ALA K:14 , THR K:126 , GLY K:127 , ARG K:160 , MG K:462 , HOH K:535 , HOH K:536BINDING SITE FOR RESIDUE PO4 K 361
4AC4SOFTWAREASP K:12 , ALA K:14 , ASP K:186 , PO4 K:361 , HOH K:535BINDING SITE FOR RESIDUE MG K 462

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IOF)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:160 -Pro A:161
2Arg K:160 -Pro K:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IOF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IOF)

(-) Exons   (0, 0)

(no "Exon" information available for 2IOF)

(-) 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:256
 aligned with PHNX_BACCE | O31156 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:256
                                    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 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIE 257
               SCOP domains d2iofa_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2iofA01            2iofA02 A:24-101 Putative phosphatase; domain 2                               2iofA01 A:5-23,A:102-260  [code=3.40.50.1000, no name defined]                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.............hhhhhhhhhhh.....hhhhhh.......hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh...eeee....hhhhhhhhhhhhh.......ee.hhhhh......hhhhhhhhhhhh......eeeee.hhhhhhhhhh...eeeee....................hhhhhhhhhhhhhhh....eee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iof A   5 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIE 260
                                    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 K from PDB  Type:PROTEIN  Length:256
 aligned with PHNX_BACCE | O31156 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:256
                                    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 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIE 257
               SCOP domains d2iofk_ K: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2iofK01            2iofK02 K:24-101 Putative phosphatase; domain 2                               2iofK01 K:5-23,K:102-260  [code=3.40.50.1000, no name defined]                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...........hhhhhhhhhhhh......hhhhhh.......hhhhhhh..hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhh........hhhhh......hhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iof K   5 KIEAVIFDWAGTTVDYGCFAPLEVFMEIFHKRGVAITAEEARKPMGLLkIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYKPDFLVTPDDVPAGRPYPWMCYKNAMELGVYPMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLTEEEVENMDSVELREKIEVVRNRFVENGAHFTIETMQELESVMEHIE 260
                                    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      
                                                                           53-LDH
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "Pfam Domain" information available for 2IOF)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,K   (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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        PHNX_BACCE | O31156: 1fez 1rdf 1rql 1rqn 1swv 1sww 2ioh

(-) Related Entries Specified in the PDB File

2ioh