OXC_OXAFO
ID OXC_OXAFO Reviewed; 568 AA.
AC P40149;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=Oxalyl-CoA decarboxylase;
DE EC=4.1.1.8;
GN Name=oxc;
OS Oxalobacter formigenes.
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Oxalobacteraceae; Oxalobacter.
OX NCBI_TaxID=847;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PARTIAL PROTEIN SEQUENCE.
RX PubMed=8157618; DOI=10.1128/jb.176.8.2468-2472.1994;
RA Lung H.-Y., Baetz A.L., Peck A.B.;
RT "Molecular cloning, DNA sequence, and gene expression of the oxalyl-
RT coenzyme A decarboxylase gene, oxc, from the bacterium Oxalobacter
RT formigenes.";
RL J. Bacteriol. 176:2468-2472(1994).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.73 ANGSTROMS) IN COMPLEX WITH THIAMINE
RP PYROPHOSPHATE; ADP AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND SUBUNIT.
RX PubMed=16216870; DOI=10.1074/jbc.m509921200;
RA Berthold C.L., Moussatche P., Richards N.G., Lindqvist Y.;
RT "Structural basis for activation of the thiamin diphosphate-dependent
RT enzyme oxalyl-CoA decarboxylase by adenosine diphosphate.";
RL J. Biol. Chem. 280:41645-41654(2005).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.82 ANGSTROMS) IN COMPLEX WITH THIAMINE
RP PYROPHOSPHATE; SUBSTRATE ANALOGS; ADP AND MAGNESIUM, FUNCTION, CATALYTIC
RP ACTIVITY, MUTAGENESIS OF GLU-56; TYR-120; GLU-121; TYR-483; SER-553 AND
RP ARG-555, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND SUBUNIT.
RX PubMed=17637344; DOI=10.1016/j.str.2007.06.001;
RA Berthold C.L., Toyota C.G., Moussatche P., Wood M.D., Leeper F.,
RA Richards N.G., Lindqvist Y.;
RT "Crystallographic snapshots of oxalyl-CoA decarboxylase give insights into
RT catalysis by nonoxidative ThDP-dependent decarboxylases.";
RL Structure 15:853-861(2007).
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). Essential enzyme for the bacterium survival, as it
CC relies on oxalic acid as its sole source of energy. Catalyzes the
CC decarboxylation of oxalyl-CoA to yield carbon dioxide and formyl-CoA.
CC {ECO:0000269|PubMed:16216870, ECO:0000269|PubMed:17637344}.
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; Evidence={ECO:0000269|PubMed:16216870,
CC ECO:0000269|PubMed:17637344};
CC -!- COFACTOR:
CC Name=a metal cation; Xref=ChEBI:CHEBI:25213;
CC Note=Binds 1 metal ion per subunit.;
CC -!- COFACTOR:
CC Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937;
CC Note=Binds 1 thiamine pyrophosphate per subunit.;
CC -!- ACTIVITY REGULATION: Inhibited by CoA and activated by ADP.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=23 uM for oxalyl-CoA (at pH 6.7 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:16216870, ECO:0000269|PubMed:17637344};
CC Note=kcat is 88 sec(-1) for decarboxylase activity with oxalyl-CoA as
CC substrate (at pH 6.7 and 30 degrees Celsius).;
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:16216870,
CC ECO:0000269|PubMed:17637344}.
CC -!- INTERACTION:
CC P40149; P40149: oxc; NbExp=2; IntAct=EBI-15648203, EBI-15648203;
CC -!- PTM: The N-terminus is blocked.
CC -!- SIMILARITY: Belongs to the TPP enzyme family. {ECO:0000305}.
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DR EMBL; M77128; AAA53683.1; -; Genomic_DNA.
DR PIR; A55219; A55219.
DR RefSeq; WP_005881708.1; NZ_CP042242.1.
DR PDB; 2C31; X-ray; 1.73 A; A/B=1-568.
DR PDB; 2JI6; X-ray; 2.06 A; A/B=1-568.
DR PDB; 2JI7; X-ray; 1.82 A; A/B=1-568.
DR PDB; 2JI8; X-ray; 2.15 A; A/B=1-568.
DR PDB; 2JI9; X-ray; 2.20 A; A/B=1-568.
DR PDB; 2JIB; X-ray; 2.20 A; A/B=1-568.
DR PDBsum; 2C31; -.
DR PDBsum; 2JI6; -.
DR PDBsum; 2JI7; -.
DR PDBsum; 2JI8; -.
DR PDBsum; 2JI9; -.
DR PDBsum; 2JIB; -.
DR AlphaFoldDB; P40149; -.
DR SMR; P40149; -.
DR DIP; DIP-29437N; -.
DR KEGG; ofo:BRW83_0575; -.
DR BioCyc; MetaCyc:MON-16180; -.
DR BRENDA; 4.1.1.8; 4478.
DR SABIO-RK; P40149; -.
DR UniPathway; UPA00540; UER00599.
DR EvolutionaryTrace; P40149; -.
DR GO; GO:0043531; F:ADP binding; IDA:UniProtKB.
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:UniProtKB.
DR GO; GO:0030976; F:thiamine pyrophosphate binding; IDA:UniProtKB.
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; Direct protein sequencing; Lyase; Magnesium;
KW Metal-binding; Nucleotide-binding; Thiamine pyrophosphate.
FT CHAIN 1..568
FT /note="Oxalyl-CoA decarboxylase"
FT /id="PRO_0000090823"
FT BINDING 34
FT /ligand="substrate"
FT BINDING 120
FT /ligand="substrate"
FT BINDING 160
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:16216870,
FT ECO:0000269|PubMed:17637344"
FT BINDING 222
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:16216870,
FT ECO:0000269|PubMed:17637344"
FT BINDING 263..267
FT /ligand="substrate"
FT BINDING 282
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:16216870,
FT ECO:0000269|PubMed:17637344"
FT BINDING 306
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:16216870,
FT ECO:0000269|PubMed:17637344"
FT BINDING 326
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:16216870,
FT ECO:0000269|PubMed:17637344"
FT BINDING 358
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 377
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000269|PubMed:16216870,
FT ECO:0000269|PubMed:17637344"
FT BINDING 401..403
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT BINDING 408..409
FT /ligand="substrate"
FT BINDING 426..428
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT BINDING 452
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:16216870,
FT ECO:0000269|PubMed:17637344"
FT BINDING 453..454
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT BINDING 479
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:16216870,
FT ECO:0000269|PubMed:17637344"
FT BINDING 481
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:16216870,
FT ECO:0000269|PubMed:17637344"
FT BINDING 483
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000269|PubMed:16216870,
FT ECO:0000269|PubMed:17637344"
FT BINDING 553..555
FT /ligand="substrate"
FT MUTAGEN 56
FT /note="E->A: Loss of the decarboxylase activity. The mutant
FT forms a dimer and not a tetramer."
FT /evidence="ECO:0000269|PubMed:17637344"
FT MUTAGEN 120
FT /note="Y->A: 3-fold reduction in the affinity binding and
FT strong reduction in the catalytic efficiency for oxalyl-
FT CoA."
FT /evidence="ECO:0000269|PubMed:17637344"
FT MUTAGEN 120
FT /note="Y->F: 2 and 12-fold reduction in the affinity
FT binding and in the catalytic efficiency for oxalyl-CoA,
FT respectively."
FT /evidence="ECO:0000269|PubMed:17637344"
FT MUTAGEN 121
FT /note="E->A: 2-fold reduction in the affinity binding and
FT strong reduction in the catalytic efficiency for oxalyl-
FT CoA."
FT /evidence="ECO:0000269|PubMed:17637344"
FT MUTAGEN 121
FT /note="E->Q: Slight increase of the affinity binding and
FT strong reduction in the catalytic efficiency for oxalyl-
FT CoA."
FT /evidence="ECO:0000269|PubMed:17637344"
FT MUTAGEN 483
FT /note="Y->A: Does not affect oxalyl-CoA binding, but it
FT strongly reduces the catalytic efficiency for oxalyl-CoA."
FT /evidence="ECO:0000269|PubMed:17637344"
FT MUTAGEN 483
FT /note="Y->F: 2-fold reduction in the affinity binding and
FT strong reduction in the catalytic efficiency for oxalyl-
FT CoA."
FT /evidence="ECO:0000269|PubMed:17637344"
FT MUTAGEN 553
FT /note="S->A: Does not affect oxalyl-CoA binding, but it
FT reduces 7-fold the catalytic efficiency for oxalyl-CoA."
FT /evidence="ECO:0000269|PubMed:17637344"
FT MUTAGEN 555
FT /note="R->A: 3-fold reduction in the affinity binding for
FT oxalyl-CoA, but it does not affect the catalytic
FT efficiency."
FT /evidence="ECO:0000269|PubMed:17637344"
FT STRAND 9..11
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 12..22
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:2C31"
FT TURN 34..36
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 37..45
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 49..52
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 56..70
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 74..78
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 81..97
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 101..107
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 110..114
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 125..128
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 130..132
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 133..138
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 142..144
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 145..157
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 158..160
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 163..169
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 171..174
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 176..178
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 179..185
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 190..193
FT /evidence="ECO:0007829|PDB:2JI9"
FT HELIX 200..211
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 214..220
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 222..227
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 230..240
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 244..246
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 248..250
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 263..265
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 266..272
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 274..280
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 285..290
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 293..295
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 301..307
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 309..311
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 314..316
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 319..324
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 326..337
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 345..367
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 377..390
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 393..401
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 402..410
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 419..422
FT /evidence="ECO:0007829|PDB:2C31"
FT TURN 423..426
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 431..442
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 446..451
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 452..456
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 459..461
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 462..467
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 472..483
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 505..510
FT /evidence="ECO:0007829|PDB:2C31"
FT TURN 511..513
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 515..521
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 522..535
FT /evidence="ECO:0007829|PDB:2C31"
FT STRAND 539..545
FT /evidence="ECO:0007829|PDB:2C31"
FT HELIX 554..559
FT /evidence="ECO:0007829|PDB:2JI7"
SQ SEQUENCE 568 AA; 60684 MW; E33DB2E0064497D1 CRC64;
MSNDDNVELT DGFHVLIDAL KMNDIDTMYG VVGIPITNLA RMWQDDGQRF YSFRHEQHAG
YAASIAGYIE GKPGVCLTVS APGFLNGVTS LAHATTNCFP MILLSGSSER EIVDLQQGDY
EEMDQMNVAR PHCKASFRIN SIKDIPIGIA RAVRTAVSGR PGGVYVDLPA KLFGQTISVE
EANKLLFKPI DPAPAQIPAE DAIARAADLI KNAKRPVIML GKGAAYAQCD DEIRALVEET
GIPFLPMGMA KGLLPDNHPQ SAAATRAFAL AQCDVCVLIG ARLNWLMQHG KGKTWGDELK
KYVQIDIQAN EMDSNQPIAA PVVGDIKSAV SLLRKALKGA PKADAEWTGA LKAKVDGNKA
KLAGKMTAET PSGMMNYSNS LGVVRDFMLA NPDISLVNEG ANALDNTRMI VDMLKPRKRL
DSGTWGVMGI GMGYCVAAAA VTGKPVIAVE GDSAFGFSGM ELETICRYNL PVTVIIMNNG
GIYKGNEADP QPGVISCTRL TRGRYDMMME AFGGKGYVAN TPAELKAALE EAVASGKPCL
INAMIDPDAG VESGRIKSLN VVSKVGKK
