PHNY_RHIME
ID PHNY_RHIME Reviewed; 485 AA.
AC Q92UV7;
DT 16-JAN-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=Phosphonoacetaldehyde dehydrogenase {ECO:0000303|PubMed:24361046};
DE EC=1.2.1.- {ECO:0000269|PubMed:24361046};
GN Name=phnY; ORFNames=SMb21539 {ECO:0000305};
OS Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium
OS meliloti).
OG Plasmid pSymB (megaplasmid 2) {ECO:0000312|Proteomes:UP000001976}.
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Sinorhizobium/Ensifer group; Sinorhizobium.
OX NCBI_TaxID=266834 {ECO:0000312|Proteomes:UP000001976};
RN [1] {ECO:0000312|EMBL:CAC49379.1, ECO:0000312|Proteomes:UP000001976}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1021 {ECO:0000312|EMBL:CAC49379.1,
RC ECO:0000312|Proteomes:UP000001976};
RX PubMed=11481431; DOI=10.1073/pnas.161294698;
RA Finan T.M., Weidner S., Wong K., Buhrmester J., Chain P., Vorhoelter F.J.,
RA Hernandez-Lucas I., Becker A., Cowie A., Gouzy J., Golding B., Puehler A.;
RT "The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing
RT endosymbiont Sinorhizobium meliloti.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:9889-9894(2001).
RN [2] {ECO:0000312|Proteomes:UP000001976}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1021 {ECO:0000312|Proteomes:UP000001976};
RX PubMed=11474104; DOI=10.1126/science.1060966;
RA Galibert F., Finan T.M., Long S.R., Puehler A., Abola P., Ampe F.,
RA Barloy-Hubler F., Barnett M.J., Becker A., Boistard P., Bothe G.,
RA Boutry M., Bowser L., Buhrmester J., Cadieu E., Capela D., Chain P.,
RA Cowie A., Davis R.W., Dreano S., Federspiel N.A., Fisher R.F., Gloux S.,
RA Godrie T., Goffeau A., Golding B., Gouzy J., Gurjal M., Hernandez-Lucas I.,
RA Hong A., Huizar L., Hyman R.W., Jones T., Kahn D., Kahn M.L., Kalman S.,
RA Keating D.H., Kiss E., Komp C., Lelaure V., Masuy D., Palm C., Peck M.C.,
RA Pohl T.M., Portetelle D., Purnelle B., Ramsperger U., Surzycki R.,
RA Thebault P., Vandenbol M., Vorhoelter F.J., Weidner S., Wells D.H.,
RA Wong K., Yeh K.-C., Batut J.;
RT "The composite genome of the legume symbiont Sinorhizobium meliloti.";
RL Science 293:668-672(2001).
RN [3] {ECO:0007744|PDB:4I3T, ECO:0007744|PDB:4I3U, ECO:0007744|PDB:4I3V, ECO:0007744|PDB:4I3W, ECO:0007744|PDB:4I3X}
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEXES WITH NAD;
RP PHOSPHONOACETALDEHYDE AND PHOSPHONOACETATE, CATALYTIC ACTIVITY, FUNCTION,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, MUTAGENESIS OF ARG-108; ASN-158;
RP GLU-254; ARG-290; CYS-291; GLU-385 AND ARG-447, AND ACTIVE SITE.
RX PubMed=24361046; DOI=10.1016/j.chembiol.2013.11.006;
RA Agarwal V., Peck S.C., Chen J.H., Borisova S.A., Chekan J.R.,
RA van der Donk W.A., Nair S.K.;
RT "Structure and function of phosphonoacetaldehyde dehydrogenase: the missing
RT link in phosphonoacetate formation.";
RL Chem. Biol. 21:125-135(2014).
CC -!- FUNCTION: Plays an important role in phosphonate degradation by
CC catalyzing the NAD-dependent conversion of phosphonoacetaldehyde (PnAA)
CC to phosphonoacetate (PnA). Has low in vitro activity with the related
CC compounds phosphonopropionaldehyde (3-oxopropyl phosphonate) and
CC glyceraldehyde 3-phosphate. {ECO:0000269|PubMed:24361046}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + NAD(+) + phosphonoacetaldehyde = 2 H(+) + NADH +
CC phosphonoacetate; Xref=Rhea:RHEA:58152, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57488, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945, ChEBI:CHEBI:58383;
CC Evidence={ECO:0000269|PubMed:24361046};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=3.2 uM for phosphonoacetaldehyde {ECO:0000269|PubMed:24361046};
CC KM=58 uM for NAD {ECO:0000269|PubMed:24361046};
CC Note=kcat is 2.2 sec(-1) with phosphonoacetaldehyde as substrate.
CC {ECO:0000269|PubMed:24361046};
CC -!- PATHWAY: Phosphorus metabolism. {ECO:0000269|PubMed:24361046}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:24361046}.
CC -!- SIMILARITY: Belongs to the aldehyde dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; AL591985; CAC49379.1; -; Genomic_DNA.
DR PIR; C95964; C95964.
DR RefSeq; NP_437519.1; NC_003078.1.
DR RefSeq; WP_010975823.1; NC_003078.1.
DR PDB; 4I3T; X-ray; 2.10 A; A/B/C/D/E/F/G/H=1-485.
DR PDB; 4I3U; X-ray; 2.10 A; A/B/C/D/E/F/G/H=1-485.
DR PDB; 4I3V; X-ray; 2.00 A; A/B/C/D/E/F/G/H=1-485.
DR PDB; 4I3W; X-ray; 2.24 A; A/B/C/D/E/F/G/H=1-485.
DR PDB; 4I3X; X-ray; 2.07 A; A/B/C/D/E/F/G/H=1-485.
DR PDBsum; 4I3T; -.
DR PDBsum; 4I3U; -.
DR PDBsum; 4I3V; -.
DR PDBsum; 4I3W; -.
DR PDBsum; 4I3X; -.
DR AlphaFoldDB; Q92UV7; -.
DR SMR; Q92UV7; -.
DR STRING; 266834.SM_b21539; -.
DR EnsemblBacteria; CAC49379; CAC49379; SM_b21539.
DR GeneID; 61600944; -.
DR KEGG; sme:SM_b21539; -.
DR PATRIC; fig|266834.11.peg.5906; -.
DR eggNOG; COG1012; Bacteria.
DR HOGENOM; CLU_005391_1_0_5; -.
DR OMA; SGQICNA; -.
DR BioCyc; MetaCyc:MON-16711; -.
DR BRENDA; 1.2.1.3; 5347.
DR Proteomes; UP000001976; Plasmid pSymB.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0016620; F:oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor; IEA:InterPro.
DR CDD; cd07146; ALDH_PhpJ; 1.
DR Gene3D; 3.40.309.10; -; 1.
DR Gene3D; 3.40.605.10; -; 1.
DR InterPro; IPR016161; Ald_DH/histidinol_DH.
DR InterPro; IPR016163; Ald_DH_C.
DR InterPro; IPR029510; Ald_DH_CS_GLU.
DR InterPro; IPR016162; Ald_DH_N.
DR InterPro; IPR015590; Aldehyde_DH_dom.
DR InterPro; IPR017656; Put_phosphonoacetaldehyde_DH.
DR Pfam; PF00171; Aldedh; 1.
DR SUPFAM; SSF53720; SSF53720; 1.
DR TIGRFAMs; TIGR03250; PhnAcAld_DH; 1.
DR PROSITE; PS00687; ALDEHYDE_DEHYDR_GLU; 1.
PE 1: Evidence at protein level;
KW 3D-structure; NAD; Nucleotide-binding; Oxidoreductase; Plasmid;
KW Reference proteome.
FT CHAIN 1..485
FT /note="Phosphonoacetaldehyde dehydrogenase"
FT /id="PRO_0000446063"
FT ACT_SITE 254
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10007,
FT ECO:0000269|PubMed:24361046"
FT ACT_SITE 291
FT /note="Nucleophile"
FT /evidence="ECO:0000269|PubMed:24361046"
FT BINDING 108
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24361046,
FT ECO:0007744|PDB:4I3X"
FT BINDING 155..157
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:24361046,
FT ECO:0007744|PDB:4I3V, ECO:0007744|PDB:4I3W,
FT ECO:0007744|PDB:4I3X"
FT BINDING 159
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24361046,
FT ECO:0007744|PDB:4I3X"
FT BINDING 181..184
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:24361046,
FT ECO:0007744|PDB:4I3V, ECO:0007744|PDB:4I3W,
FT ECO:0007744|PDB:4I3X"
FT BINDING 235
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:24361046,
FT ECO:0007744|PDB:4I3V, ECO:0007744|PDB:4I3W,
FT ECO:0007744|PDB:4I3X"
FT BINDING 290..292
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24361046,
FT ECO:0007744|PDB:4I3X"
FT BINDING 385
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:24361046,
FT ECO:0007744|PDB:4I3X"
FT BINDING 447
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24361046,
FT ECO:0007744|PDB:4I3X"
FT MUTAGEN 108
FT /note="R->A: Decreased catalytic activity and decreased
FT affinity for phosphonoacetaldehyde."
FT /evidence="ECO:0000269|PubMed:24361046"
FT MUTAGEN 158
FT /note="N->A: Strongly decreased catalytic activity."
FT /evidence="ECO:0000269|PubMed:24361046"
FT MUTAGEN 254
FT /note="E->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:24361046"
FT MUTAGEN 290
FT /note="R->A: Decreased catalytic activity and slightly
FT decreased affinity for phosphonoacetaldehyde."
FT /evidence="ECO:0000269|PubMed:24361046"
FT MUTAGEN 291
FT /note="C->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:24361046"
FT MUTAGEN 385
FT /note="E->A: Decreased catalytic activity and decreased
FT affinity for phosphonoacetaldehyde."
FT /evidence="ECO:0000269|PubMed:24361046"
FT MUTAGEN 447
FT /note="R->A: Decreased catalytic activity and strongly
FT decreased affinity for phosphonoacetaldehyde."
FT /evidence="ECO:0000269|PubMed:24361046"
FT STRAND 15..17
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 20..22
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 25..31
FT /evidence="ECO:0007829|PDB:4I3V"
FT TURN 33..35
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 38..43
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 47..59
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 66..82
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 84..95
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 99..119
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 126..129
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 138..147
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 151..155
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 157..159
FT /evidence="ECO:0007829|PDB:4I3X"
FT HELIX 162..173
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 178..182
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 188..199
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 204..206
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 207..209
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 214..223
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 228..234
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 236..245
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 249..254
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 259..263
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 269..284
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 285..288
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 293..300
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 301..316
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 336..351
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 355..358
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 371..374
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 380..383
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 391..396
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 400..407
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 410..414
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 417..419
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 423..432
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 435..440
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 457..459
FT /evidence="ECO:0007829|PDB:4I3U"
FT STRAND 460..462
FT /evidence="ECO:0007829|PDB:4I3V"
FT HELIX 467..473
FT /evidence="ECO:0007829|PDB:4I3V"
FT STRAND 475..483
FT /evidence="ECO:0007829|PDB:4I3V"
SQ SEQUENCE 485 AA; 52913 MW; 974DC1DFDC5EC51E CRC64;
MTNAEVTIAV RHEPMRIAGR LVDTDDRVEV RYPWNDTVVG TVPAGRAEHA REAFAIAAAY
QPKLTRYERQ KILLATAEAL AARKEEISDV ITLELGISKA DSLYEVGRAF DVFTLAGQMC
IRDDGEIFSC DLTPHGKARK IFTMREPLTA ISAITPFNHP LNMVAHKVAP AIATNNCVVV
KPTELTPMTA LLLADILYEA GLPPEMLSVV TGWPADIGME MITNPHVDLV TFTGSVPVGK
LIAANAHYKR QVLELGGNDP LIILNDLSDD DLARAADLAV AGATKNSGQR CTAVKRILCQ
ESVADRFVPL VLERAKRLRF GDPMDRSTDL GTVIHEKAAA LFEERVMRAA EEGADILYHP
GRSGALLPPI VVDRVPHQSD LVLEETFGPI IPIVRVPDDD DATITLSNST AFGLSSGVCT
NDYRRMQKYI AGLKVGTVNI WEVPGYRIEM SPFGGIKDSG NGYKEGVIEA MKSFTNVKTF
SLPWP
