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Protein

Phosphonoacetaldehyde hydrolase

Gene

phnX

Organism
Bacillus cereus
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in phosphonate degradation.

Catalytic activityi

Phosphonoacetaldehyde + H2O = acetaldehyde + phosphate.

Cofactori

Mg2+Note: Binds 1 Mg2+ ion per subunit.

Kineticsi

  1. KM=33 µM for phosphonoacetaldehyde (at pH 7.0, 25 degrees Celsius)

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei9 – 91Nucleophile
    Metal bindingi9 – 91Magnesium
    Metal bindingi11 – 111Magnesium; via carbonyl oxygen
    Active sitei50 – 501Schiff-base intermediate with substrate
    Metal bindingi183 – 1831Magnesium

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Magnesium, Metal-binding, Schiff base

    Enzyme and pathway databases

    BRENDAi3.11.1.1. 648.
    SABIO-RKO31156.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Phosphonoacetaldehyde hydrolase (EC:3.11.1.1)
    Short name:
    Phosphonatase
    Alternative name(s):
    Phosphonoacetaldehyde phosphonohydrolase
    Gene namesi
    Name:phnX
    OrganismiBacillus cereus
    Taxonomic identifieri1396 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillusBacillus cereus group

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi9 – 91D → A: Loss of enzymatic activity. 2 Publications
    Mutagenesisi9 – 91D → E: Kcat/KM decreases 30000-fold. 2 Publications
    Mutagenesisi19 – 191C → A or S: Kcat/KM decreases 10-100-fold. 1 Publication
    Mutagenesisi46 – 461M → L: Kcat/KM decreases 17000-fold. 1 Publication
    Mutagenesisi47 – 471G → A: Kcat/KM decreases 10000-fold. 1 Publication
    Mutagenesisi47 – 471G → P or V: Loss of enzymatic activity. 1 Publication
    Mutagenesisi50 – 501K → R: Loss of enzymatic activity. 1 Publication
    Mutagenesisi53 – 531H → A: Kcat/KM decreases 1000-fold. 2 Publications
    Mutagenesisi53 – 531H → Q: Kcat/KM decreases 250-fold. 2 Publications
    Mutagenesisi125 – 1251Y → A: Kcat/KM decreases 230-fold. 1 Publication
    Mutagenesisi125 – 1251Y → F: Kcat/KM decreases 10-fold. 1 Publication
    Mutagenesisi183 – 1831D → A: Loss of enzymatic activity. 1 Publication
    Mutagenesisi187 – 1871D → A: Kcat/KM decreases 10000-fold. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 264264Phosphonoacetaldehyde hydrolasePRO_0000284575Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.4 Publications

    Protein-protein interaction databases

    STRINGi226900.BC1326.

    Structurei

    Secondary structure

    1
    264
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 84Combined sources
    Turni11 – 133Combined sources
    Beta strandi14 – 163Combined sources
    Helixi23 – 319Combined sources
    Turni32 – 343Combined sources
    Helixi39 – 435Combined sources
    Turni44 – 474Combined sources
    Helixi50 – 5910Combined sources
    Helixi61 – 7111Combined sources
    Helixi77 – 9418Combined sources
    Helixi95 – 984Combined sources
    Helixi105 – 11410Combined sources
    Beta strandi118 – 1225Combined sources
    Helixi127 – 13913Combined sources
    Beta strandi145 – 1473Combined sources
    Helixi150 – 1523Combined sources
    Beta strandi153 – 1553Combined sources
    Beta strandi157 – 1604Combined sources
    Helixi161 – 17010Combined sources
    Helixi175 – 1773Combined sources
    Beta strandi178 – 1847Combined sources
    Helixi185 – 1939Combined sources
    Beta strandi196 – 2016Combined sources
    Turni206 – 2083Combined sources
    Helixi212 – 2176Combined sources
    Helixi220 – 23617Combined sources
    Beta strandi240 – 2456Combined sources
    Helixi246 – 2483Combined sources
    Helixi249 – 2568Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1FEZX-ray3.00A/B/C/D2-257[»]
    1RDFX-ray2.80A/B/C/D/E/F1-264[»]
    1RQLX-ray2.40A/B1-264[»]
    1RQNX-ray2.80A/B1-264[»]
    1SWVX-ray2.30A/B1-264[»]
    1SWWX-ray2.30A/B1-264[»]
    2IOFX-ray2.50A/K1-264[»]
    2IOHX-ray2.90A/B/C/D1-264[»]
    ProteinModelPortaliO31156.
    SMRiO31156. Positions 2-257.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO31156.

    Family & Domainsi

    Sequence similaritiesi

    Family and domain databases

    Gene3Di1.10.150.240. 1 hit.
    3.40.50.1000. 2 hits.
    HAMAPiMF_01375. PhnX.
    InterProiIPR023214. HAD-like_dom.
    IPR006439. HAD-SF_hydro_IA.
    IPR023198. PGP_dom2.
    IPR006323. Phosphonoacetald_hydro.
    [Graphical view]
    PfamiPF13419. HAD_2. 1 hit.
    [Graphical view]
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR01549. HAD-SF-IA-v1. 1 hit.
    TIGR01509. HAD-SF-IA-v3. 1 hit.
    TIGR01422. phosphonatase. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    O31156-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKIEAVIFDW AGTTVDYGCF APLEVFMEIF HKRGVAITAE EARKPMGLLK
    60 70 80 90 100
    IDHVRALTEM PRIASEWNRV FRQLPTEADI QEMYEEFEEI LFAILPRYAS
    110 120 130 140 150
    PINGVKEVIA SLRERGIKIG STTGYTREMM DIVAKEAALQ GYKPDFLVTP
    160 170 180 190 200
    DDVPAGRPYP WMCYKNAMEL GVYPMNHMIK VGDTVSDMKE GRNAGMWTVG
    210 220 230 240 250
    VILGSSELGL TEEEVENMDS VELREKIEVV RNRFVENGAH FTIETMQELE
    260
    SVMEHIEKQE LIIS
    Length:264
    Mass (Da):30,060
    Last modified:April 17, 2007 - v3
    Checksum:i59A99D2BBED760AD
    GO

    Sequence cautioni

    The sequence AAB86434.2 differs from that shown. Reason: Erroneous initiation. Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF030979 Genomic DNA. Translation: AAB86434.2. Different initiation.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF030979 Genomic DNA. Translation: AAB86434.2. Different initiation.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1FEZX-ray3.00A/B/C/D2-257[»]
    1RDFX-ray2.80A/B/C/D/E/F1-264[»]
    1RQLX-ray2.40A/B1-264[»]
    1RQNX-ray2.80A/B1-264[»]
    1SWVX-ray2.30A/B1-264[»]
    1SWWX-ray2.30A/B1-264[»]
    2IOFX-ray2.50A/K1-264[»]
    2IOHX-ray2.90A/B/C/D1-264[»]
    ProteinModelPortaliO31156.
    SMRiO31156. Positions 2-257.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi226900.BC1326.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    BRENDAi3.11.1.1. 648.
    SABIO-RKO31156.

    Miscellaneous databases

    EvolutionaryTraceiO31156.

    Family and domain databases

    Gene3Di1.10.150.240. 1 hit.
    3.40.50.1000. 2 hits.
    HAMAPiMF_01375. PhnX.
    InterProiIPR023214. HAD-like_dom.
    IPR006439. HAD-SF_hydro_IA.
    IPR023198. PGP_dom2.
    IPR006323. Phosphonoacetald_hydro.
    [Graphical view]
    PfamiPF13419. HAD_2. 1 hit.
    [Graphical view]
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR01549. HAD-SF-IA-v1. 1 hit.
    TIGR01509. HAD-SF-IA-v3. 1 hit.
    TIGR01422. phosphonatase. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    1. "Insights into the mechanism of catalysis by the P-C bond-cleaving enzyme phosphonoacetaldehyde hydrolase derived from gene sequence analysis and mutagenesis."
      Baker A.S., Ciocci M.J., Metcalf W.W., Kim J., Babbitt P.C., Wanner B.L., Martin B.M., Dunaway-Mariano D.
      Biochemistry 37:9305-9315(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-17 AND 35-55, REACTION MECHANISM, BIOPHYSICAL CHARACTERIZATION.
      Strain: ATCC 43881 / AI-2.
    2. "Investigation of the substrate binding and catalytic groups of the P-C bond cleaving enzyme, phosphonoacetaldehyde hydrolase."
      Olsen D.B., Hepburn T.W., Lee S.-L., Martin B.M., Mariano P.S., Dunaway-Mariano D.
      Arch. Biochem. Biophys. 296:144-151(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 34-55, SCHIFF BASE, REACTION MECHANISM.
      Strain: ATCC 43881 / AI-2.
    3. "Crystallization and preliminary crystallographic analysis of phosphonoacetaldehyde hydrolase."
      Morais M.C., Baker A.S., Dunaway-Mariano D., Allen K.N.
      Acta Crystallogr. D 56:206-209(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT, PRELIMINARY CRYSTALLOGRAPHY.
      Strain: ATCC 43881 / AI-2.
    4. "The crystal structure of Bacillus cereus phosphonoacetaldehyde hydrolase: insight into catalysis of phosphorus bond cleavage and catalytic diversification within the HAD enzyme superfamily."
      Morais M.C., Zhang W., Baker A.S., Zhang G., Dunaway-Mariano D., Allen K.N.
      Biochemistry 39:10385-10396(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 2-260 IN COMPLEX WITH THE PHOSPHATE ANALOG TUNGSTATE, BINDING OF MAGNESIUM, MUTAGENESIS OF ASP-9.
      Strain: ATCC 43881 / AI-2.
    5. "X-ray crystallographic and site-directed mutagenesis analysis of the mechanism of Schiff-base formation in phosphonoacetaldehyde hydrolase catalysis."
      Morais M.C., Zhang G., Zhang W., Olsen D.B., Dunaway-Mariano D., Allen K.N.
      J. Biol. Chem. 279:9353-9361(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH MG(2+) AND WITH MG(2+) PLUS VINYLSULFONATE, MUTAGENESIS OF CYS-19; MET-46; HIS-53 AND TYR-125.
      Strain: ATCC 43881 / AI-2.
    6. "Analysis of the substrate specificity loop of the HAD superfamily cap domain."
      Lahiri S.D., Zhang G., Dai J., Dunaway-Mariano D., Allen K.N.
      Biochemistry 43:2812-2820(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF MUTANT PRO-47, MUTAGENESIS OF GLY-47 AND LYS-50.
      Strain: ATCC 43881 / AI-2.
    7. "Investigation of metal ion binding in phosphonoacetaldehyde hydrolase identifies sequence markers for metal-activated enzymes of the HAD enzyme superfamily."
      Zhang G., Morais M.C., Dai J., Zhang W., Dunaway-Mariano D., Allen K.N.
      Biochemistry 43:4990-4997(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF MUTANT ALA-9 IN COMPLEX WITH MG(2+) AND WITH MG(2+) PLUS PHOSPHONOACETALDEHYDE, MUTAGENESIS OF ASP-9; ASP-183 AND ASP-187.
      Strain: ATCC 43881 / AI-2.
    8. "Diversification of function in the haloacid dehalogenase enzyme superfamily: the role of the cap domain in hydrolytic phosphorus--carbon bond cleavage."
      Lahiri S.D., Zhang G., Dunaway-Mariano D., Allen K.N.
      Bioorg. Chem. 34:394-409(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF MUTANT ARG-50, MUTAGENESIS OF HIS-53.
      Strain: ATCC 43881 / AI-2.

    Entry informationi

    Entry nameiPHNX_BACCE
    AccessioniPrimary (citable) accession number: O31156
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 17, 2007
    Last sequence update: April 17, 2007
    Last modified: June 24, 2015
    This is version 72 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.