PHNX_BACCE
ID PHNX_BACCE Reviewed; 264 AA.
AC O31156;
DT 17-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 17-APR-2007, sequence version 3.
DT 03-AUG-2022, entry version 106.
DE RecName: Full=Phosphonoacetaldehyde hydrolase;
DE Short=Phosphonatase;
DE EC=3.11.1.1;
DE AltName: Full=Phosphonoacetaldehyde phosphonohydrolase;
GN Name=phnX;
OS Bacillus cereus.
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus;
OC Bacillus cereus group.
OX NCBI_TaxID=1396;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-17 AND 35-55,
RP REACTION MECHANISM, AND BIOPHYSICAL CHARACTERIZATION.
RC STRAIN=ATCC 43881 / AI-2;
RX PubMed=9649311; DOI=10.1021/bi972677d;
RA Baker A.S., Ciocci M.J., Metcalf W.W., Kim J., Babbitt P.C., Wanner B.L.,
RA Martin B.M., Dunaway-Mariano D.;
RT "Insights into the mechanism of catalysis by the P-C bond-cleaving enzyme
RT phosphonoacetaldehyde hydrolase derived from gene sequence analysis and
RT mutagenesis.";
RL Biochemistry 37:9305-9315(1998).
RN [2]
RP PROTEIN SEQUENCE OF 34-55, SCHIFF BASE, AND REACTION MECHANISM.
RC STRAIN=ATCC 43881 / AI-2;
RX PubMed=1605625; DOI=10.1016/0003-9861(92)90556-c;
RA Olsen D.B., Hepburn T.W., Lee S.-L., Martin B.M., Mariano P.S.,
RA Dunaway-Mariano D.;
RT "Investigation of the substrate binding and catalytic groups of the P-C
RT bond cleaving enzyme, phosphonoacetaldehyde hydrolase.";
RL Arch. Biochem. Biophys. 296:144-151(1992).
RN [3]
RP SUBUNIT, AND PRELIMINARY CRYSTALLOGRAPHY.
RC STRAIN=ATCC 43881 / AI-2;
RX PubMed=10666607; DOI=10.1107/s0907444999015899;
RA Morais M.C., Baker A.S., Dunaway-Mariano D., Allen K.N.;
RT "Crystallization and preliminary crystallographic analysis of
RT phosphonoacetaldehyde hydrolase.";
RL Acta Crystallogr. D 56:206-209(2000).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 2-260 IN COMPLEX WITH THE
RP PHOSPHATE ANALOG TUNGSTATE, BINDING OF MAGNESIUM, AND MUTAGENESIS OF ASP-9.
RC STRAIN=ATCC 43881 / AI-2;
RX PubMed=10956028; DOI=10.1021/bi001171j;
RA Morais M.C., Zhang W., Baker A.S., Zhang G., Dunaway-Mariano D.,
RA Allen K.N.;
RT "The crystal structure of Bacillus cereus phosphonoacetaldehyde hydrolase:
RT insight into catalysis of phosphorus bond cleavage and catalytic
RT diversification within the HAD enzyme superfamily.";
RL Biochemistry 39:10385-10396(2000).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH MG(2+) AND WITH
RP MG(2+) PLUS VINYLSULFONATE, AND MUTAGENESIS OF CYS-19; MET-46; HIS-53 AND
RP TYR-125.
RC STRAIN=ATCC 43881 / AI-2;
RX PubMed=14670958; DOI=10.1074/jbc.m312345200;
RA Morais M.C., Zhang G., Zhang W., Olsen D.B., Dunaway-Mariano D.,
RA Allen K.N.;
RT "X-ray crystallographic and site-directed mutagenesis analysis of the
RT mechanism of Schiff-base formation in phosphonoacetaldehyde hydrolase
RT catalysis.";
RL J. Biol. Chem. 279:9353-9361(2004).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF MUTANT PRO-47, AND MUTAGENESIS OF
RP GLY-47 AND LYS-50.
RC STRAIN=ATCC 43881 / AI-2;
RX PubMed=15005616; DOI=10.1021/bi0356810;
RA Lahiri S.D., Zhang G., Dai J., Dunaway-Mariano D., Allen K.N.;
RT "Analysis of the substrate specificity loop of the HAD superfamily cap
RT domain.";
RL Biochemistry 43:2812-2820(2004).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF MUTANT ALA-9 IN COMPLEX WITH
RP MG(2+) AND WITH MG(2+) PLUS PHOSPHONOACETALDEHYDE, AND MUTAGENESIS OF
RP ASP-9; ASP-183 AND ASP-187.
RC STRAIN=ATCC 43881 / AI-2;
RX PubMed=15109258; DOI=10.1021/bi036309n;
RA Zhang G., Morais M.C., Dai J., Zhang W., Dunaway-Mariano D., Allen K.N.;
RT "Investigation of metal ion binding in phosphonoacetaldehyde hydrolase
RT identifies sequence markers for metal-activated enzymes of the HAD enzyme
RT superfamily.";
RL Biochemistry 43:4990-4997(2004).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF MUTANT ARG-50, AND MUTAGENESIS OF
RP HIS-53.
RC STRAIN=ATCC 43881 / AI-2;
RX PubMed=17070898; DOI=10.1016/j.bioorg.2006.09.007;
RA Lahiri S.D., Zhang G., Dunaway-Mariano D., Allen K.N.;
RT "Diversification of function in the haloacid dehalogenase enzyme
RT superfamily: the role of the cap domain in hydrolytic phosphorus-carbon
RT bond cleavage.";
RL Bioorg. Chem. 34:394-409(2006).
CC -!- FUNCTION: Involved in phosphonate degradation.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + phosphonoacetaldehyde = acetaldehyde + H(+) + phosphate;
CC Xref=Rhea:RHEA:18905, ChEBI:CHEBI:15343, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:43474, ChEBI:CHEBI:58383; EC=3.11.1.1;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Note=Binds 1 Mg(2+) ion per subunit.;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=33 uM for phosphonoacetaldehyde (at pH 7.0, 25 degrees Celsius);
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10666607,
CC ECO:0000269|PubMed:10956028, ECO:0000269|PubMed:14670958,
CC ECO:0000269|PubMed:15109258}.
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily. PhnX family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB86434.2; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AF030979; AAB86434.2; ALT_INIT; Genomic_DNA.
DR RefSeq; WP_000687366.1; NZ_VEPS02000001.1.
DR PDB; 1FEZ; X-ray; 3.00 A; A/B/C/D=2-257.
DR PDB; 1RDF; X-ray; 2.80 A; A/B/C/D/E/F=1-264.
DR PDB; 1RQL; X-ray; 2.40 A; A/B=1-264.
DR PDB; 1RQN; X-ray; 2.80 A; A/B=1-264.
DR PDB; 1SWV; X-ray; 2.30 A; A/B=1-264.
DR PDB; 1SWW; X-ray; 2.30 A; A/B=1-264.
DR PDB; 2IOF; X-ray; 2.50 A; A/K=1-264.
DR PDB; 2IOH; X-ray; 2.90 A; A/B/C/D=1-264.
DR PDBsum; 1FEZ; -.
DR PDBsum; 1RDF; -.
DR PDBsum; 1RQL; -.
DR PDBsum; 1RQN; -.
DR PDBsum; 1SWV; -.
DR PDBsum; 1SWW; -.
DR PDBsum; 2IOF; -.
DR PDBsum; 2IOH; -.
DR AlphaFoldDB; O31156; -.
DR SMR; O31156; -.
DR DrugBank; DB03635; Ethanesulfonic acid.
DR DrugBank; DB03174; Phosphonoacetaldehyde.
DR DrugBank; DB04359; Vinylsulfonic acid.
DR PRIDE; O31156; -.
DR PATRIC; fig|1396.434.peg.1664; -.
DR BRENDA; 3.11.1.1; 648.
DR SABIO-RK; O31156; -.
DR EvolutionaryTrace; O31156; -.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0050194; F:phosphonoacetaldehyde hydrolase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0019700; P:organic phosphonate catabolic process; IEA:InterPro.
DR CDD; cd02586; HAD_PHN; 1.
DR Gene3D; 1.10.150.240; -; 1.
DR Gene3D; 3.40.50.1000; -; 1.
DR HAMAP; MF_01375; PhnX; 1.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006439; HAD-SF_hydro_IA.
DR InterPro; IPR041492; HAD_2.
DR InterPro; IPR023214; HAD_sf.
DR InterPro; IPR023198; PGP-like_dom2.
DR InterPro; IPR006323; Phosphonoacetald_hydro.
DR Pfam; PF13419; HAD_2; 1.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01549; HAD-SF-IA-v1; 1.
DR TIGRFAMs; TIGR01509; HAD-SF-IA-v3; 1.
DR TIGRFAMs; TIGR01422; phosphonatase; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Hydrolase; Magnesium;
KW Metal-binding; Schiff base.
FT CHAIN 1..264
FT /note="Phosphonoacetaldehyde hydrolase"
FT /id="PRO_0000284575"
FT ACT_SITE 9
FT /note="Nucleophile"
FT ACT_SITE 50
FT /note="Schiff-base intermediate with substrate"
FT BINDING 9
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 11
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 183
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT MUTAGEN 9
FT /note="D->A: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:10956028,
FT ECO:0000269|PubMed:15109258"
FT MUTAGEN 9
FT /note="D->E: Kcat/KM decreases 30000-fold."
FT /evidence="ECO:0000269|PubMed:10956028,
FT ECO:0000269|PubMed:15109258"
FT MUTAGEN 19
FT /note="C->A,S: Kcat/KM decreases 10-100-fold."
FT /evidence="ECO:0000269|PubMed:14670958"
FT MUTAGEN 46
FT /note="M->L: Kcat/KM decreases 17000-fold."
FT /evidence="ECO:0000269|PubMed:14670958"
FT MUTAGEN 47
FT /note="G->A: Kcat/KM decreases 10000-fold."
FT /evidence="ECO:0000269|PubMed:15005616"
FT MUTAGEN 47
FT /note="G->P,V: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:15005616"
FT MUTAGEN 50
FT /note="K->R: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:15005616"
FT MUTAGEN 53
FT /note="H->A: Kcat/KM decreases 1000-fold."
FT /evidence="ECO:0000269|PubMed:14670958,
FT ECO:0000269|PubMed:17070898"
FT MUTAGEN 53
FT /note="H->Q: Kcat/KM decreases 250-fold."
FT /evidence="ECO:0000269|PubMed:14670958,
FT ECO:0000269|PubMed:17070898"
FT MUTAGEN 125
FT /note="Y->A: Kcat/KM decreases 230-fold."
FT /evidence="ECO:0000269|PubMed:14670958"
FT MUTAGEN 125
FT /note="Y->F: Kcat/KM decreases 10-fold."
FT /evidence="ECO:0000269|PubMed:14670958"
FT MUTAGEN 183
FT /note="D->A: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:15109258"
FT MUTAGEN 187
FT /note="D->A: Kcat/KM decreases 10000-fold."
FT /evidence="ECO:0000269|PubMed:15109258"
FT STRAND 5..8
FT /evidence="ECO:0007829|PDB:1SWV"
FT TURN 11..13
FT /evidence="ECO:0007829|PDB:1SWV"
FT STRAND 14..16
FT /evidence="ECO:0007829|PDB:1SWV"
FT HELIX 23..31
FT /evidence="ECO:0007829|PDB:1SWV"
FT TURN 32..34
FT /evidence="ECO:0007829|PDB:1SWV"
FT HELIX 39..43
FT /evidence="ECO:0007829|PDB:1SWV"
FT TURN 44..47
FT /evidence="ECO:0007829|PDB:1SWV"
FT HELIX 50..59
FT /evidence="ECO:0007829|PDB:1SWV"
FT HELIX 61..71
FT /evidence="ECO:0007829|PDB:1SWV"
FT HELIX 77..94
FT /evidence="ECO:0007829|PDB:1SWV"
FT HELIX 95..98
FT /evidence="ECO:0007829|PDB:1SWV"
FT HELIX 105..114
FT /evidence="ECO:0007829|PDB:1SWV"
FT STRAND 118..122
FT /evidence="ECO:0007829|PDB:1SWV"
FT HELIX 127..139
FT /evidence="ECO:0007829|PDB:1SWV"
FT STRAND 145..147
FT /evidence="ECO:0007829|PDB:2IOF"
FT HELIX 150..152
FT /evidence="ECO:0007829|PDB:1SWV"
FT STRAND 153..155
FT /evidence="ECO:0007829|PDB:1RDF"
FT STRAND 157..160
FT /evidence="ECO:0007829|PDB:2IOH"
FT HELIX 161..170
FT /evidence="ECO:0007829|PDB:1SWV"
FT HELIX 175..177
FT /evidence="ECO:0007829|PDB:1SWV"
FT STRAND 178..184
FT /evidence="ECO:0007829|PDB:1SWV"
FT HELIX 185..193
FT /evidence="ECO:0007829|PDB:1SWV"
FT STRAND 196..201
FT /evidence="ECO:0007829|PDB:1SWV"
FT TURN 206..208
FT /evidence="ECO:0007829|PDB:1SWV"
FT HELIX 212..217
FT /evidence="ECO:0007829|PDB:1SWV"
FT HELIX 220..236
FT /evidence="ECO:0007829|PDB:1SWV"
FT STRAND 240..245
FT /evidence="ECO:0007829|PDB:1SWV"
FT HELIX 246..248
FT /evidence="ECO:0007829|PDB:1SWV"
FT HELIX 249..256
FT /evidence="ECO:0007829|PDB:1SWV"
SQ SEQUENCE 264 AA; 30060 MW; 59A99D2BBED760AD CRC64;
MKIEAVIFDW AGTTVDYGCF APLEVFMEIF HKRGVAITAE EARKPMGLLK IDHVRALTEM
PRIASEWNRV FRQLPTEADI QEMYEEFEEI LFAILPRYAS PINGVKEVIA SLRERGIKIG
STTGYTREMM DIVAKEAALQ GYKPDFLVTP DDVPAGRPYP WMCYKNAMEL GVYPMNHMIK
VGDTVSDMKE GRNAGMWTVG VILGSSELGL TEEEVENMDS VELREKIEVV RNRFVENGAH
FTIETMQELE SVMEHIEKQE LIIS
