PRPF_SHEON
ID PRPF_SHEON Reviewed; 397 AA.
AC Q8EJW4;
DT 29-APR-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 97.
DE RecName: Full=2-methyl-aconitate isomerase {ECO:0000303|PubMed:17567742};
DE EC=5.3.3.- {ECO:0000269|PubMed:17567742};
DE AltName: Full=Cis-trans isomerase {ECO:0000303|PubMed:17567742};
GN Name=prpF; OrderedLocusNames=SO_0342;
OS Shewanella oneidensis (strain MR-1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC Shewanellaceae; Shewanella.
OX NCBI_TaxID=211586;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MR-1;
RX PubMed=12368813; DOI=10.1038/nbt749;
RA Heidelberg J.F., Paulsen I.T., Nelson K.E., Gaidos E.J., Nelson W.C.,
RA Read T.D., Eisen J.A., Seshadri R., Ward N.L., Methe B.A., Clayton R.A.,
RA Meyer T., Tsapin A., Scott J., Beanan M.J., Brinkac L.M., Daugherty S.C.,
RA DeBoy R.T., Dodson R.J., Durkin A.S., Haft D.H., Kolonay J.F., Madupu R.,
RA Peterson J.D., Umayam L.A., White O., Wolf A.M., Vamathevan J.J.,
RA Weidman J.F., Impraim M., Lee K., Berry K.J., Lee C., Mueller J.,
RA Khouri H.M., Gill J., Utterback T.R., McDonald L.A., Feldblyum T.V.,
RA Smith H.O., Venter J.C., Nealson K.H., Fraser C.M.;
RT "Genome sequence of the dissimilatory metal ion-reducing bacterium
RT Shewanella oneidensis.";
RL Nat. Biotechnol. 20:1118-1123(2002).
RN [2]
RP FUNCTION.
RC STRAIN=MR-1;
RX PubMed=14702315; DOI=10.1128/jb.186.2.454-462.2004;
RA Grimek T.L., Escalante-Semerena J.C.;
RT "The acnD genes of Shewenella oneidensis and Vibrio cholerae encode a new
RT Fe/S-dependent 2-methylcitrate dehydratase enzyme that requires prpF
RT function in vivo.";
RL J. Bacteriol. 186:454-462(2004).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.57 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG,
RP FUNCTION, CATALYTIC ACTIVITY, OXIDATION AT CYS-107, SUBUNIT, AND REACTION
RP MECHANISM.
RC STRAIN=MR-1;
RX PubMed=17567742; DOI=10.1110/ps.072801907;
RA Garvey G.S., Rocco C.J., Escalante-Semerena J.C., Rayment I.;
RT "The three-dimensional crystal structure of the PrpF protein of Shewanella
RT oneidensis complexed with trans-aconitate: insights into its biological
RT function.";
RL Protein Sci. 16:1274-1284(2007).
CC -!- FUNCTION: Involved in the catabolism of short chain fatty acids (SCFA)
CC via the 2-methylcitrate cycle II (propionate degradation route). PrpF
CC catalyzes the cis-trans isomerization of 2-methyl-aconitate through a
CC base-catalyzed proton abstraction coupled with a rotation about C2-C3
CC bond of 2-methyl-aconitate. {ECO:0000269|PubMed:14702315,
CC ECO:0000269|PubMed:17567742}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-methyl-trans-aconitate = 2-methyl-cis-aconitate;
CC Xref=Rhea:RHEA:37751, ChEBI:CHEBI:57872, ChEBI:CHEBI:58915;
CC Evidence={ECO:0000269|PubMed:17567742};
CC -!- PATHWAY: Organic acid metabolism; propanoate degradation.
CC {ECO:0000305|PubMed:14702315}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:17567742}.
CC -!- MISCELLANEOUS: Together with AcnD, they are able to restore the growth
CC of prpD mutant on propionate. {ECO:0000269|PubMed:14702315}.
CC -!- SIMILARITY: Belongs to the PrpF family. {ECO:0000305}.
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DR EMBL; AE014299; AAN53427.1; -; Genomic_DNA.
DR RefSeq; NP_715982.1; NC_004347.2.
DR RefSeq; WP_011070707.1; NZ_CP053946.1.
DR PDB; 2PVZ; X-ray; 1.97 A; A/B=1-397.
DR PDB; 2PW0; X-ray; 1.57 A; A/B=1-397.
DR PDB; 5K87; X-ray; 1.22 A; A/B=2-397.
DR PDBsum; 2PVZ; -.
DR PDBsum; 2PW0; -.
DR PDBsum; 5K87; -.
DR AlphaFoldDB; Q8EJW4; -.
DR SMR; Q8EJW4; -.
DR STRING; 211586.SO_0342; -.
DR PaxDb; Q8EJW4; -.
DR KEGG; son:SO_0342; -.
DR PATRIC; fig|211586.12.peg.332; -.
DR eggNOG; COG2828; Bacteria.
DR HOGENOM; CLU_026443_2_0_6; -.
DR OMA; VPATYMR; -.
DR OrthoDB; 1328531at2; -.
DR PhylomeDB; Q8EJW4; -.
DR BioCyc; SONE211586:G1GMP-327-MON; -.
DR BRENDA; 5.2.1.B4; 5706.
DR BRENDA; 5.3.3.7; 5706.
DR UniPathway; UPA00946; -.
DR EvolutionaryTrace; Q8EJW4; -.
DR Proteomes; UP000008186; Chromosome.
DR GO; GO:0016863; F:intramolecular oxidoreductase activity, transposing C=C bonds; IDA:UniProtKB.
DR GO; GO:0019629; P:propionate catabolic process, 2-methylcitrate cycle; IDA:UniProtKB.
DR InterPro; IPR012709; PrpF.
DR InterPro; IPR007400; PrpF_protein.
DR PANTHER; PTHR43709; PTHR43709; 1.
DR Pfam; PF04303; PrpF; 1.
DR TIGRFAMs; TIGR02334; prpF; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Isomerase; Oxidation; Reference proteome.
FT CHAIN 1..397
FT /note="2-methyl-aconitate isomerase"
FT /id="PRO_0000432936"
FT ACT_SITE 107
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:17567742"
FT ACT_SITE 321
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:17567742"
FT BINDING 22
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17567742"
FT BINDING 69..73
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17567742"
FT BINDING 109
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17567742"
FT BINDING 281
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17567742"
FT BINDING 312
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17567742"
FT BINDING 317
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17567742"
FT BINDING 322
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17567742"
FT MOD_RES 107
FT /note="Cysteine sulfinic acid (-SO2H)"
FT /evidence="ECO:0000269|PubMed:17567742"
FT STRAND 10..19
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 22..28
FT /evidence="ECO:0007829|PDB:5K87"
FT HELIX 29..31
FT /evidence="ECO:0007829|PDB:5K87"
FT HELIX 34..37
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 38..40
FT /evidence="ECO:0007829|PDB:5K87"
FT HELIX 41..51
FT /evidence="ECO:0007829|PDB:5K87"
FT HELIX 69..71
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 72..79
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 86..94
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 96..99
FT /evidence="ECO:0007829|PDB:5K87"
FT TURN 108..110
FT /evidence="ECO:0007829|PDB:2PW0"
FT HELIX 111..120
FT /evidence="ECO:0007829|PDB:5K87"
FT HELIX 126..128
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 131..141
FT /evidence="ECO:0007829|PDB:5K87"
FT TURN 142..145
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 146..155
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 177..183
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 194..196
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 201..207
FT /evidence="ECO:0007829|PDB:5K87"
FT TURN 208..210
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 211..228
FT /evidence="ECO:0007829|PDB:5K87"
FT HELIX 229..232
FT /evidence="ECO:0007829|PDB:5K87"
FT HELIX 240..243
FT /evidence="ECO:0007829|PDB:5K87"
FT HELIX 247..263
FT /evidence="ECO:0007829|PDB:5K87"
FT HELIX 270..274
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 278..287
FT /evidence="ECO:0007829|PDB:5K87"
FT HELIX 301..303
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 305..312
FT /evidence="ECO:0007829|PDB:5K87"
FT HELIX 322..332
FT /evidence="ECO:0007829|PDB:5K87"
FT HELIX 338..342
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 349..355
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 358..369
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 372..382
FT /evidence="ECO:0007829|PDB:5K87"
FT STRAND 384..394
FT /evidence="ECO:0007829|PDB:5K87"
SQ SEQUENCE 397 AA; 41660 MW; CE63C499806398B9 CRC64;
MSNKLFPPQI KVAATYMRGG TSKGVFFRLQ DLPEAAQVPG PARDALLLRV IGSPDPYAKQ
IDGMGGATSS TSKTVILSHS SKANHDVDYL FGQVSIDKPF VDWSGNCGNL TAAVGAFAIS
NGLIDAARIP RNGVCTVRIW QANIGKTIIA HVPITDGAVQ ETGDFELDGV TFPAAEVQIE
FMNPAADDDG EGGCMFPTGN LVDVLEVPGI GRFNATMINA GIPTIFINAE DLGYTGTELQ
DDINSDNAAL AKFETIRAHG ALRMGLIKHI DEAASRQHTP KIAFVAPPKS YASSSGKTVA
AEDVDLLVRA LSMGKLHHAM MGTAAVAIGT AAAIPGTLVN LAAGGGEKEA VRFGHPSGTL
RVGAQAVQEN GEWTVIKAIM SRSARVLMEG FVRVPKP
