ODH_YERPE
ID ODH_YERPE Reviewed; 456 AA.
AC Q8CKU7; Q74VP6;
DT 08-MAY-2019, integrated into UniProtKB/Swiss-Prot.
DT 08-MAY-2019, sequence version 2.
DT 03-AUG-2022, entry version 105.
DE RecName: Full=Yersinopine synthase {ECO:0000305|PubMed:29618515};
DE EC=1.5.1.- {ECO:0000269|PubMed:29618515};
DE AltName: Full=Opine dehydrogenase {ECO:0000303|PubMed:29618515};
DE Short=ODH {ECO:0000303|PubMed:29618515};
DE AltName: Full=Yersinopine dehydrogenase {ECO:0000303|PubMed:29618515};
GN OrderedLocusNames=y2835 {ECO:0000312|EMBL:AAM86386.1},
GN YP_1249 {ECO:0000312|EMBL:AAS61492.1};
OS Yersinia pestis.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Yersinia.
OX NCBI_TaxID=632;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=KIM10+ / Biovar Mediaevalis;
RX PubMed=12142430; DOI=10.1128/jb.184.16.4601-4611.2002;
RA Deng W., Burland V., Plunkett G. III, Boutin A., Mayhew G.F., Liss P.,
RA Perna N.T., Rose D.J., Mau B., Zhou S., Schwartz D.C., Fetherston J.D.,
RA Lindler L.E., Brubaker R.R., Plano G.V., Straley S.C., McDonough K.A.,
RA Nilles M.L., Matson J.S., Blattner F.R., Perry R.D.;
RT "Genome sequence of Yersinia pestis KIM.";
RL J. Bacteriol. 184:4601-4611(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=91001 / Biovar Mediaevalis;
RX PubMed=15368893; DOI=10.1093/dnares/11.3.179;
RA Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D.,
RA Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L.,
RA Dai R., Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H.,
RA Wang J., Huang P., Yang R.;
RT "Complete genome sequence of Yersinia pestis strain 91001, an isolate
RT avirulent to humans.";
RL DNA Res. 11:179-197(2004).
RN [3] {ECO:0007744|PDB:6C4L, ECO:0007744|PDB:6C4M}
RP X-RAY CRYSTALLOGRAPHY (1.94 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH
RP NADP, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBSTRATE SPECIFICITY, SUBUNIT, AND ACTIVE SITE.
RX PubMed=29618515; DOI=10.1074/jbc.ra118.002007;
RA McFarlane J.S., Davis C.L., Lamb A.L.;
RT "Staphylopine, pseudopaline, and yersinopine dehydrogenases: A structural
RT and kinetic analysis of a new functional class of opine dehydrogenase.";
RL J. Biol. Chem. 293:8009-8019(2018).
CC -!- FUNCTION: Catalyzes the NADPH-dependent reductive condensation of
CC pyruvate to the intermediate formed by the adjacently encoded enzyme
CC y2836, namely (2S)-2-amino-4-{[(1S)-1-carboxy-2-(1H-imidazol-4-
CC yl)ethyl]amino}butanoate, leading to the production of yersinopine.
CC This is the last step in the biosynthesis of the metallophore
CC yersinopine, which is involved in metal acquisition and thus enables
CC bacterial growth inside the host, where metal access is limited.
CC Therefore, this enzyme probably contributes to Yersinia virulence.
CC Cannot use alpha-ketoglutarate in place of pyruvate, and displays only
CC poor efficiency with oxaloacetate and glyoxylate.
CC {ECO:0000269|PubMed:29618515}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + NADP(+) + yersinopine = (2S)-2-amino-4-{[(1S)-1-carboxy-
CC 2-(1H-imidazol-4-yl)ethyl]amino}butanoate + H(+) + NADPH + pyruvate;
CC Xref=Rhea:RHEA:59792, ChEBI:CHEBI:15361, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349,
CC ChEBI:CHEBI:143196, ChEBI:CHEBI:143224;
CC Evidence={ECO:0000269|PubMed:29618515};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:59794;
CC Evidence={ECO:0000305|PubMed:29618515};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=73 uM for pyruvate (at pH 8.0 and 22 degrees Celsius)
CC {ECO:0000269|PubMed:29618515};
CC KM=1900 uM for oxaloacetate (at pH 8.0 and 22 degrees Celsius)
CC {ECO:0000269|PubMed:29618515};
CC KM=1900 uM for glyoxylate (at pH 8.0 and 22 degrees Celsius)
CC {ECO:0000269|PubMed:29618515};
CC Note=kcat is 0.30 sec(-1) with pyruvate as substrate. kcat is 0.29
CC sec(-1) with oxaloacetate as substrate. kcat is 0.22 sec(-1) with
CC glyoxylate as substrate (at pH 8.0 and 22 degrees Celsius).
CC {ECO:0000269|PubMed:29618515};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:29618515}.
CC -!- SIMILARITY: Belongs to the staphylopine dehydrogenase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAM86386.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAS61492.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AE009952; AAM86386.1; ALT_INIT; Genomic_DNA.
DR EMBL; AE017042; AAS61492.1; ALT_INIT; Genomic_DNA.
DR RefSeq; WP_002211373.1; NZ_WUCM01000027.1.
DR PDB; 6C4L; X-ray; 2.00 A; C=1-456.
DR PDB; 6C4M; X-ray; 1.94 A; C=1-456.
DR PDBsum; 6C4L; -.
DR PDBsum; 6C4M; -.
DR AlphaFoldDB; Q8CKU7; -.
DR SMR; Q8CKU7; -.
DR STRING; 214092.YPO1347; -.
DR DNASU; 1147782; -.
DR EnsemblBacteria; AAM86386; AAM86386; y2835.
DR EnsemblBacteria; AAS61492; AAS61492; YP_1249.
DR GeneID; 66842192; -.
DR KEGG; ypk:y2835; -.
DR KEGG; ypm:YP_1249; -.
DR HOGENOM; CLU_637619_0_0_6; -.
DR OMA; RMPKEDY; -.
DR Proteomes; UP000001019; Chromosome.
DR Proteomes; UP000002490; Chromosome.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR016935; Opine_metallophore_DH.
DR Pfam; PF10100; Staph_opine_DH; 1.
DR PIRSF; PIRSF029692; UCP029692; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
PE 1: Evidence at protein level;
KW 3D-structure; NADP; Oxidoreductase.
FT CHAIN 1..456
FT /note="Yersinopine synthase"
FT /id="PRO_0000447041"
FT ACT_SITE 242
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:29618515"
FT BINDING 12..15
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:29618515"
FT BINDING 35..40
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:29618515"
FT BINDING 154
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:29618515"
FT HELIX 2..4
FT /evidence="ECO:0007829|PDB:6C4M"
FT STRAND 7..10
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 14..26
FT /evidence="ECO:0007829|PDB:6C4M"
FT STRAND 31..34
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 39..50
FT /evidence="ECO:0007829|PDB:6C4M"
FT STRAND 53..58
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 60..64
FT /evidence="ECO:0007829|PDB:6C4M"
FT STRAND 68..72
FT /evidence="ECO:0007829|PDB:6C4M"
FT STRAND 74..78
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 80..82
FT /evidence="ECO:0007829|PDB:6C4M"
FT STRAND 89..92
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 96..98
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 99..103
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 108..110
FT /evidence="ECO:0007829|PDB:6C4M"
FT STRAND 116..119
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 126..136
FT /evidence="ECO:0007829|PDB:6C4M"
FT STRAND 142..149
FT /evidence="ECO:0007829|PDB:6C4M"
FT STRAND 151..155
FT /evidence="ECO:0007829|PDB:6C4M"
FT STRAND 185..191
FT /evidence="ECO:0007829|PDB:6C4M"
FT STRAND 193..199
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 207..217
FT /evidence="ECO:0007829|PDB:6C4M"
FT TURN 218..220
FT /evidence="ECO:0007829|PDB:6C4M"
FT STRAND 222..225
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 229..233
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 237..246
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 249..256
FT /evidence="ECO:0007829|PDB:6C4M"
FT TURN 269..271
FT /evidence="ECO:0007829|PDB:6C4M"
FT STRAND 272..275
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 276..295
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 303..310
FT /evidence="ECO:0007829|PDB:6C4M"
FT TURN 316..318
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 321..326
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 327..329
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 332..346
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 363..365
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 383..401
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 407..427
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 429..431
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 434..436
FT /evidence="ECO:0007829|PDB:6C4M"
FT HELIX 441..453
FT /evidence="ECO:0007829|PDB:6C4M"
SQ SEQUENCE 456 AA; 50860 MW; BDA4F3B2B73B8485 CRC64;
MHNTLPTLIL GAGPAAIQLA VDISATGDAR LGLYNRPSTK GERLKQYLAL TPTLYLQGTG
KAQATQKESS VTIDCYIDQL AQAVGDWQRL ILAVPADHYY AVLQQIPWAA LPQLKSVILL
SSSMGSGLMV QNLLNAAGKR DVEVISLSSY YADTKYIRAE TQDISANTQD INAGTQDIGA
IQPYRAYTKA FKQRIYLANQ WGNAGSAEMS WLTAVLARHH IDTLPCSNLL AAERFSITNY
VHPPLALADT TLQALFYPEQ RSQYLYKTQP EGPVCPAVIA DLAGLADDYK RLLNRLGVEE
INLLRFLNDD NYPVPASMVS RRWIDEFPQL PPLEQQYALF VRYTALLVDP YSTPDEQGRF
YDFSAVKVAT VYQDANALWH LPRVPLEDVH KLRTLLLLAG ALDVVMPTAQ RLLQRFQQAL
KAFIDRVGEE HCHPSLLGDD CDRQAAIIEQ QWRSQT
