OXC_ECOLI
ID OXC_ECOLI Reviewed; 564 AA.
AC P0AFI0; P78093; P78194; P78195;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Oxalyl-CoA decarboxylase;
DE EC=4.1.1.8;
GN Name=oxc; Synonyms=yfdU; OrderedLocusNames=b2373, JW2370;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP INDUCTION.
RX PubMed=23335415; DOI=10.1128/jb.01936-12;
RA Fontenot E.M., Ezelle K.E., Gabreski L.N., Giglio E.R., McAfee J.M.,
RA Mills A.C., Qureshi M.N., Salmon K.M., Toyota C.G.;
RT "YfdW and YfdU are required for oxalate-induced acid tolerance in
RT Escherichia coli K-12.";
RL J. Bacteriol. 195:1446-1455(2013).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.74 ANGSTROMS) IN COMPLEX WITH THIAMINE
RP PYROPHOSPHATE; SUBSTRATE ANALOGS; ADP AND MAGNESIUM, FUNCTION, CATALYTIC
RP ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION, COFACTOR, AND
RP SUBUNIT.
RX PubMed=20553497; DOI=10.1111/j.1742-4658.2010.07673.x;
RA Werther T., Zimmer A., Wille G., Golbik R., Weiss M.S., Konig S.;
RT "New insights into structure-function relationships of oxalyl CoA
RT decarboxylase from Escherichia coli.";
RL FEBS J. 277:2628-2640(2010).
CC -!- FUNCTION: Involved in the catabolism of oxalate and in the adapatation
CC to low pH via the induction of the oxalate-dependent acid tolerance
CC response (ATR). Catalyzes the decarboxylation of oxalyl-CoA to yield
CC carbon dioxide and formyl-CoA. {ECO:0000269|PubMed:20553497}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + oxalyl-CoA = CO2 + formyl-CoA; Xref=Rhea:RHEA:19333,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:57376,
CC ChEBI:CHEBI:57388; EC=4.1.1.8;
CC Evidence={ECO:0000269|PubMed:20553497};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:20553497};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:20553497};
CC -!- COFACTOR:
CC Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937;
CC Evidence={ECO:0000269|PubMed:20553497};
CC Note=Binds 1 thiamine pyrophosphate per subunit.
CC {ECO:0000269|PubMed:20553497};
CC -!- ACTIVITY REGULATION: Activated by ADP. {ECO:0000269|PubMed:20553497}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=3.17 uM for oxalyl-CoA (with 300 uM ADP at pH 6.5 and 30 degrees
CC Celsius) {ECO:0000269|PubMed:20553497};
CC KM=4.8 uM for oxalyl-CoA (at pH 6.5 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:20553497};
CC Note=kcat is 69.7 sec(-1) for decarboxylase activity with oxalyl-CoA
CC as substrate (with 300 uM ADP at pH 6.5 and 30 degrees Celsius). kcat
CC is 60.7 sec(-1) for decarboxylase activity with oxalyl-CoA as
CC substrate (at pH 6.5 and 30 degrees Celsius).;
CC pH dependence:
CC Optimum pH is between 5.5 and 7. {ECO:0000269|PubMed:20553497};
CC -!- PATHWAY: Metabolic intermediate degradation; oxalate degradation; CO(2)
CC and formate from oxalate: step 2/2.
CC -!- SUBUNIT: Homotetramer; dimer of dimers. {ECO:0000269|PubMed:20553497}.
CC -!- INTERACTION:
CC P0AFI0; P0AFI0: oxc; NbExp=4; IntAct=EBI-557143, EBI-557143;
CC -!- INDUCTION: By the acid response regulator EvgA.
CC {ECO:0000269|PubMed:23335415}.
CC -!- SIMILARITY: Belongs to the TPP enzyme family. {ECO:0000305}.
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DR EMBL; U00096; AAC75432.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16245.1; -; Genomic_DNA.
DR PIR; B65011; B65011.
DR RefSeq; NP_416874.1; NC_000913.3.
DR RefSeq; WP_001283490.1; NZ_LN832404.1.
DR PDB; 2Q27; X-ray; 2.12 A; A/B=1-564.
DR PDB; 2Q28; X-ray; 1.74 A; A/B=1-564.
DR PDB; 2Q29; X-ray; 1.82 A; A/B=1-564.
DR PDBsum; 2Q27; -.
DR PDBsum; 2Q28; -.
DR PDBsum; 2Q29; -.
DR AlphaFoldDB; P0AFI0; -.
DR SMR; P0AFI0; -.
DR BioGRID; 4260862; 15.
DR BioGRID; 851186; 1.
DR DIP; DIP-48075N; -.
DR IntAct; P0AFI0; 6.
DR MINT; P0AFI0; -.
DR STRING; 511145.b2373; -.
DR PaxDb; P0AFI0; -.
DR PRIDE; P0AFI0; -.
DR EnsemblBacteria; AAC75432; AAC75432; b2373.
DR EnsemblBacteria; BAA16245; BAA16245; BAA16245.
DR GeneID; 946845; -.
DR KEGG; ecj:JW2370; -.
DR KEGG; eco:b2373; -.
DR PATRIC; fig|1411691.4.peg.4356; -.
DR EchoBASE; EB3895; -.
DR eggNOG; COG0028; Bacteria.
DR InParanoid; P0AFI0; -.
DR OMA; PGPYGCL; -.
DR PhylomeDB; P0AFI0; -.
DR BioCyc; EcoCyc:G7236-MON; -.
DR BioCyc; MetaCyc:G7236-MON; -.
DR BRENDA; 4.1.1.8; 2026.
DR UniPathway; UPA00540; UER00599.
DR EvolutionaryTrace; P0AFI0; -.
DR PRO; PR:P0AFI0; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0043531; F:ADP binding; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0008949; F:oxalyl-CoA decarboxylase activity; IDA:EcoCyc.
DR GO; GO:0030976; F:thiamine pyrophosphate binding; IDA:EcoCyc.
DR GO; GO:0071468; P:cellular response to acidic pH; IMP:EcoCyc.
DR GO; GO:0001561; P:fatty acid alpha-oxidation; IBA:GO_Central.
DR GO; GO:0033611; P:oxalate catabolic process; IDA:UniProtKB.
DR InterPro; IPR029035; DHS-like_NAD/FAD-binding_dom.
DR InterPro; IPR045025; HACL1-like.
DR InterPro; IPR017660; Oxalyl-CoA_decarboxylase.
DR InterPro; IPR029061; THDP-binding.
DR InterPro; IPR012000; Thiamin_PyroP_enz_cen_dom.
DR InterPro; IPR012001; Thiamin_PyroP_enz_TPP-bd_dom.
DR InterPro; IPR011766; TPP_enzyme-bd_C.
DR PANTHER; PTHR43710; PTHR43710; 1.
DR Pfam; PF02775; TPP_enzyme_C; 1.
DR Pfam; PF00205; TPP_enzyme_M; 1.
DR Pfam; PF02776; TPP_enzyme_N; 1.
DR SUPFAM; SSF52467; SSF52467; 1.
DR SUPFAM; SSF52518; SSF52518; 2.
DR TIGRFAMs; TIGR03254; oxalate_oxc; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Decarboxylase; Lyase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Thiamine pyrophosphate.
FT CHAIN 1..564
FT /note="Oxalyl-CoA decarboxylase"
FT /id="PRO_0000090824"
FT BINDING 32
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 118
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 158
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:20553497"
FT BINDING 220
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:20553497"
FT BINDING 261..265
FT /ligand="substrate"
FT /evidence="ECO:0000305"
FT BINDING 280
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:20553497"
FT BINDING 302
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:20553497"
FT BINDING 322
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:20553497"
FT BINDING 355
FT /ligand="substrate"
FT BINDING 372
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000269|PubMed:20553497"
FT BINDING 396..398
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT BINDING 403..404
FT /ligand="substrate"
FT BINDING 421..423
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT BINDING 447
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:20553497"
FT BINDING 448..449
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT BINDING 474
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:20553497"
FT BINDING 476
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:20553497"
FT BINDING 478
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000269|PubMed:20553497"
FT BINDING 550..552
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT STRAND 7..9
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 10..20
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 25..28
FT /evidence="ECO:0007829|PDB:2Q28"
FT TURN 32..34
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 35..43
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 47..50
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 54..68
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 72..76
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 79..95
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 99..105
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 108..112
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 123..127
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 128..130
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 131..136
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 140..142
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 143..155
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 156..158
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 161..167
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 168..172
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 174..176
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 177..182
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 188..191
FT /evidence="ECO:0007829|PDB:2Q29"
FT STRAND 194..196
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 198..210
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 212..218
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 220..225
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 228..238
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 242..244
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 246..248
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 261..263
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 264..270
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 272..278
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 283..288
FT /evidence="ECO:0007829|PDB:2Q28"
FT TURN 289..291
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 297..303
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 305..307
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 310..312
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 315..320
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 322..335
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 342..363
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 368..370
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 372..383
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 390..396
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 397..405
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 410..412
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 414..417
FT /evidence="ECO:0007829|PDB:2Q28"
FT TURN 418..421
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 426..437
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 441..446
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 447..451
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 454..456
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 457..462
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 467..473
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 475..478
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 502..509
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 512..516
FT /evidence="ECO:0007829|PDB:2Q28"
FT HELIX 519..532
FT /evidence="ECO:0007829|PDB:2Q28"
FT STRAND 536..542
FT /evidence="ECO:0007829|PDB:2Q28"
SQ SEQUENCE 564 AA; 60581 MW; 94418B2BE7D40C17 CRC64;
MSDQLQMTDG MHIIVEALKQ NNIDTIYGVV GIPVTDMARH AQAEGIRYIG FRHEQSAGYA
AAASGFLTQK PGICLTVSAP GFLNGLTALA NATVNGFPMI MISGSSDRAI VDLQQGDYEE
LDQMNAAKPY AKAAFRVNQP QDLGIALARA IRVSVSGRPG GVYLDLPANV LAATMEKDEA
LTTIVKVENP SPALLPCPKS VTSAISLLAK AERPLIILGK GAAYSQADEQ LREFIESAQI
PFLPMSMAKG ILEDTHPLSA AAARSFALAN ADVVMLVGAR LNWLLAHGKK GWAADTQFIQ
LDIEPQEIDS NRPIAVPVVG DIASSMQGML AELKQNTFTT PLVWRDILNI HKQQNAQKMH
EKLSTDTQPL NYFNALSAVR DVLRENQDIY LVNEGANTLD NARNIIDMYK PRRRLDCGTW
GVMGIGMGYA IGASVTSGSP VVAIEGDSAF GFSGMEIETI CRYNLPVTIV IFNNGGIYRG
DGVDLSGAGA PSPTDLLHHA RYDKLMDAFR GVGYNVTTTD ELRHALTTGI QSRKPTIINV
VIDPAAGTES GHITKLNPKQ VAGN
