PPHA_VARSP
ID PPHA_VARSP Reviewed; 290 AA.
AC Q84G06;
DT 30-NOV-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 69.
DE RecName: Full=Phosphonopyruvate hydrolase {ECO:0000303|PubMed:12697754};
DE Short=PPH {ECO:0000303|PubMed:12697754};
DE EC=3.11.1.3;
GN Name=pphA {ECO:0000303|PubMed:12697754};
GN Synonyms=palA {ECO:0000312|EMBL:AAO24736.1};
OS Variovorax sp. (strain Pal2).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Comamonadaceae; Variovorax.
OX NCBI_TaxID=218557;
RN [1] {ECO:0000305, ECO:0000312|EMBL:AAO24736.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-28; 67-84 AND
RP 109-136, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND MASS SPECTROMETRY.
RX PubMed=12697754; DOI=10.1074/jbc.m301871200;
RA Kulakova A.N., Wisdom G.B., Kulakov L.A., Quinn J.P.;
RT "The purification and characterization of phosphonopyruvate hydrolase, a
RT novel carbon-phosphorus bond cleavage enzyme from Variovorax sp Pal2.";
RL J. Biol. Chem. 278:23426-23431(2003).
RN [2] {ECO:0000305, ECO:0000312|EMBL:AAO24736.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND INDUCTION.
RX PubMed=19191873; DOI=10.1111/j.1574-6968.2008.01477.x;
RA Kulakova A.N., Kulakov L.A., Villarreal-Chiu J.F., Gilbert J.A.,
RA McGrath J.W., Quinn J.P.;
RT "Expression of the phosphonoalanine-degradative gene cluster from
RT Variovorax sp. Pal2 is induced by growth on phosphonoalanine and
RT phosphonopyruvate.";
RL FEMS Microbiol. Lett. 292:100-106(2009).
RN [3] {ECO:0000305}
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF APOENZYME AND IN COMPLEXES WITH
RP MAGNESIUM IONS; PHOSPHONOPYRUVATE AND OXALATE, BIOPHYSICOCHEMICAL
RP PROPERTIES, MUTAGENESIS OF ARG-188, AND SUBUNIT.
RX PubMed=16981709; DOI=10.1021/bi061208l;
RA Chen C.C., Han Y., Niu W., Kulakova A.N., Howard A., Quinn J.P.,
RA Dunaway-Mariano D., Herzberg O.;
RT "Structure and kinetics of phosphonopyruvate hydrolase from Variovorax sp.
RT Pal2: new insight into the divergence of catalysis within the PEP
RT mutase/isocitrate lyase superfamily.";
RL Biochemistry 45:11491-11504(2006).
CC -!- FUNCTION: Hydrolyzes phosphonopyruvate. Not active towards
CC phosphoenolpyruvate, glycerophosphate, phospho-L-serine or
CC phosphoglycolic acid. {ECO:0000269|PubMed:12697754}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-phosphonopyruvate + H2O = H(+) + phosphate + pyruvate;
CC Xref=Rhea:RHEA:16673, ChEBI:CHEBI:15361, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:43474, ChEBI:CHEBI:71402; EC=3.11.1.3;
CC Evidence={ECO:0000269|PubMed:12697754};
CC -!- COFACTOR:
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:12697754};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:12697754};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:12697754};
CC Note=Divalent metal cations. Co(2+), Mg(2+) or Mn(2+) can be used.
CC {ECO:0000269|PubMed:12697754};
CC -!- ACTIVITY REGULATION: Partially inhibited by EDTA. Activity is restored
CC by Co(2+), and to a lesser extent by Ni(2+) and Mg(2+). Unaffected by
CC Cs(2+) and Ca(2+). Activity is reduced by Mn(2+) and Cu(2+).
CC {ECO:0000269|PubMed:12697754}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.53 mM for phosphonopyruvate (at 37 degrees Celsius, pH 7.0, with
CC 5 umol CoCl(2)) {ECO:0000269|PubMed:12697754,
CC ECO:0000269|PubMed:16981709};
CC KM=19.5 uM for phosphonopyruvate (at 25 degrees Celsius, pH 7.5, with
CC 5 mM MgCl(2)) {ECO:0000269|PubMed:12697754,
CC ECO:0000269|PubMed:16981709};
CC Vmax=202 umol/min/mg enzyme (at 37 degrees Celsius, pH 7.0, with 5
CC umol CoCl(2)) {ECO:0000269|PubMed:12697754,
CC ECO:0000269|PubMed:16981709};
CC pH dependence:
CC Optimum pH is 7.0. Active from pH 6.0 to 9.0.
CC {ECO:0000269|PubMed:12697754, ECO:0000269|PubMed:16981709};
CC -!- SUBUNIT: Homodimer (PubMed:12697754). Homotetramer (PubMed:16981709).
CC {ECO:0000269|PubMed:12697754, ECO:0000269|PubMed:16981709}.
CC -!- INDUCTION: By phosphonoalanine or phosphonopyruvate.
CC {ECO:0000269|PubMed:19191873}.
CC -!- MASS SPECTROMETRY: Mass=31187; Method=MALDI;
CC Evidence={ECO:0000269|PubMed:12697754};
CC -!- SIMILARITY: Belongs to the isocitrate lyase/PEP mutase superfamily. PEP
CC mutase family. {ECO:0000255}.
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DR EMBL; AY179862; AAO24736.1; -; Genomic_DNA.
DR PDB; 2DUA; X-ray; 2.00 A; A=1-290.
DR PDB; 2HJP; X-ray; 1.90 A; A=1-290.
DR PDB; 2HRW; X-ray; 2.20 A; A=1-290.
DR PDBsum; 2DUA; -.
DR PDBsum; 2HJP; -.
DR PDBsum; 2HRW; -.
DR AlphaFoldDB; Q84G06; -.
DR SMR; Q84G06; -.
DR KEGG; ag:AAO24736; -.
DR BioCyc; MetaCyc:MON-16715; -.
DR BRENDA; 3.11.1.3; 8611.
DR EvolutionaryTrace; Q84G06; -.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0033978; F:phosphonopyruvate hydrolase activity; IDA:UniProtKB.
DR CDD; cd00377; ICL_PEPM; 1.
DR Gene3D; 3.20.20.60; -; 1.
DR InterPro; IPR039556; ICL/PEPM.
DR InterPro; IPR012649; PPH.
DR InterPro; IPR015813; Pyrv/PenolPyrv_Kinase-like_dom.
DR InterPro; IPR040442; Pyrv_Kinase-like_dom_sf.
DR SUPFAM; SSF51621; SSF51621; 1.
DR TIGRFAMs; TIGR02321; Pphn_pyruv_hyd; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cobalt; Direct protein sequencing; Hydrolase; Magnesium;
KW Metal-binding.
FT CHAIN 1..290
FT /note="Phosphonopyruvate hydrolase"
FT /id="PRO_0000401168"
FT ACT_SITE 54
FT /note="Nucleophile"
FT /evidence="ECO:0000255, ECO:0000303|PubMed:16981709"
FT BINDING 40..44
FT /ligand="substrate"
FT BINDING 81
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:16981709"
FT BINDING 155
FT /ligand="substrate"
FT BINDING 186
FT /ligand="substrate"
FT BINDING 188
FT /ligand="substrate"
FT MUTAGEN 188
FT /note="R->A: Reduced affinity for substrate."
FT /evidence="ECO:0000269|PubMed:16981709"
FT CONFLICT 132
FT /note="E -> I (in Ref. 1; AA sequence)"
FT /evidence="ECO:0000305"
FT HELIX 3..13
FT /evidence="ECO:0007829|PDB:2HJP"
FT STRAND 17..21
FT /evidence="ECO:0007829|PDB:2HJP"
FT HELIX 25..34
FT /evidence="ECO:0007829|PDB:2HJP"
FT STRAND 37..41
FT /evidence="ECO:0007829|PDB:2HJP"
FT HELIX 43..49
FT /evidence="ECO:0007829|PDB:2HJP"
FT TURN 54..56
FT /evidence="ECO:0007829|PDB:2HJP"
FT HELIX 60..71
FT /evidence="ECO:0007829|PDB:2HJP"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:2HJP"
FT TURN 83..86
FT /evidence="ECO:0007829|PDB:2HJP"
FT HELIX 89..102
FT /evidence="ECO:0007829|PDB:2HJP"
FT STRAND 105..110
FT /evidence="ECO:0007829|PDB:2HJP"
FT HELIX 131..144
FT /evidence="ECO:0007829|PDB:2HJP"
FT STRAND 150..156
FT /evidence="ECO:0007829|PDB:2HJP"
FT TURN 158..162
FT /evidence="ECO:0007829|PDB:2HJP"
FT HELIX 165..177
FT /evidence="ECO:0007829|PDB:2HJP"
FT STRAND 181..185
FT /evidence="ECO:0007829|PDB:2HJP"
FT STRAND 190..192
FT /evidence="ECO:0007829|PDB:2HJP"
FT HELIX 193..201
FT /evidence="ECO:0007829|PDB:2HJP"
FT STRAND 208..210
FT /evidence="ECO:0007829|PDB:2HJP"
FT HELIX 220..224
FT /evidence="ECO:0007829|PDB:2HJP"
FT STRAND 229..234
FT /evidence="ECO:0007829|PDB:2HJP"
FT HELIX 237..256
FT /evidence="ECO:0007829|PDB:2HJP"
FT TURN 260..265
FT /evidence="ECO:0007829|PDB:2HJP"
FT HELIX 269..275
FT /evidence="ECO:0007829|PDB:2HJP"
FT HELIX 278..288
FT /evidence="ECO:0007829|PDB:2HJP"
SQ SEQUENCE 290 AA; 31179 MW; 9B041151AE069F47 CRC64;
MTKNQALRAA LDSGRLFTAM AAHNPLVAKL AEQAGFGGIW GSGFELSASY AVPDANILSM
STHLEMMRAI ASTVSIPLIA DIDTGFGNAV NVHYVVPQYE AAGASAIVME DKTFPKDTSL
RTDGRQELVR IEEFQGKIAA ATAARADRDF VVIARVEALI AGLGQQEAVR RGQAYEEAGA
DAILIHSRQK TPDEILAFVK SWPGKVPLVL VPTAYPQLTE ADIAALSKVG IVIYGNHAIR
AAVGAVREVF ARIRRDGGIR EVDAALPSVK EIIELQGDER MRAVEARYLK
