RIB3_CANAL
ID RIB3_CANAL Reviewed; 204 AA.
AC Q5A3V6; A0A1D8PFC4; Q5A3P2;
DT 24-JUL-2007, integrated into UniProtKB/Swiss-Prot.
DT 24-JUL-2007, sequence version 2.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=3,4-dihydroxy-2-butanone 4-phosphate synthase;
DE Short=DHBP synthase;
DE EC=4.1.99.12 {ECO:0000269|PubMed:15328619};
GN Name=RIB3; OrderedLocusNames=CAALFM_C112360CA;
GN ORFNames=CaO19.12693, CaO19.5228;
OS Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Debaryomycetaceae; Candida/Lodderomyces clade; Candida.
OX NCBI_TaxID=237561;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=SC5314 / ATCC MYA-2876;
RX PubMed=15123810; DOI=10.1073/pnas.0401648101;
RA Jones T., Federspiel N.A., Chibana H., Dungan J., Kalman S., Magee B.B.,
RA Newport G., Thorstenson Y.R., Agabian N., Magee P.T., Davis R.W.,
RA Scherer S.;
RT "The diploid genome sequence of Candida albicans.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:7329-7334(2004).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=SC5314 / ATCC MYA-2876;
RX PubMed=17419877; DOI=10.1186/gb-2007-8-4-r52;
RA van het Hoog M., Rast T.J., Martchenko M., Grindle S., Dignard D.,
RA Hogues H., Cuomo C., Berriman M., Scherer S., Magee B.B., Whiteway M.,
RA Chibana H., Nantel A., Magee P.T.;
RT "Assembly of the Candida albicans genome into sixteen supercontigs aligned
RT on the eight chromosomes.";
RL Genome Biol. 8:RESEARCH52.1-RESEARCH52.12(2007).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND GENOME REANNOTATION.
RC STRAIN=SC5314 / ATCC MYA-2876;
RX PubMed=24025428; DOI=10.1186/gb-2013-14-9-r97;
RA Muzzey D., Schwartz K., Weissman J.S., Sherlock G.;
RT "Assembly of a phased diploid Candida albicans genome facilitates allele-
RT specific measurements and provides a simple model for repeat and indel
RT structure.";
RL Genome Biol. 14:RESEARCH97.1-RESEARCH97.14(2013).
RN [4] {ECO:0007744|PDB:1TKS, ECO:0007744|PDB:1TKU}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-8, X-RAY
RP CRYSTALLOGRAPHY (1.66 ANGSTROMS) IN COMPLEX WITH D-RIBULOSE 5-PHOSPHATE,
RP FUNCTION, CATALYTIC ACTIVITY, MASS SPECTROMETRY, BIOPHYSICOCHEMICAL
RP PROPERTIES, MUTAGENESIS OF TYR-87; ASP-92 AND GLU-166, SUBUNIT, AND
RP PATHWAY.
RX PubMed=15328619; DOI=10.1016/j.jmb.2004.06.053;
RA Echt S., Bauer S., Steinbacher S., Huber R., Bacher A., Fischer M.;
RT "Potential anti-infective targets in pathogenic yeasts: structure and
RT properties of 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida
RT albicans.";
RL J. Mol. Biol. 341:1085-1096(2004).
CC -!- FUNCTION: Catalyzes the conversion of D-ribulose 5-phosphate to formate
CC and 3,4-dihydroxy-2-butanone 4-phosphate.
CC {ECO:0000269|PubMed:15328619}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate +
CC formate + H(+); Xref=Rhea:RHEA:18457, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:15740, ChEBI:CHEBI:58121, ChEBI:CHEBI:58830;
CC EC=4.1.99.12; Evidence={ECO:0000269|PubMed:15328619};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:18458;
CC Evidence={ECO:0000305|PubMed:15328619};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000305|PubMed:15328619};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Note=Binds 2 divalent metal cations per subunit. Magnesium or
CC manganese. {ECO:0000250};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=37 uM for D-ribulose-5-phosphate {ECO:0000269|PubMed:15328619};
CC Vmax=332 nmol/min/mg enzyme {ECO:0000269|PubMed:15328619};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-
CC oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1.
CC {ECO:0000305|PubMed:15328619}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:15328619}.
CC -!- PTM: S-glutathionylation is reversible and dependent on a glutaredoxin.
CC {ECO:0000250|UniProtKB:Q99258}.
CC -!- MASS SPECTROMETRY: Mass=22530; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:15328619};
CC -!- SIMILARITY: Belongs to the DHBP synthase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AOW26854.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305|PubMed:15328619};
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DR EMBL; CP017623; AOW26854.1; ALT_INIT; Genomic_DNA.
DR RefSeq; XP_716297.2; XM_711204.2.
DR PDB; 1TKS; X-ray; 1.60 A; A/B=1-204.
DR PDB; 1TKU; X-ray; 1.66 A; A/B=1-204.
DR PDB; 2RIS; X-ray; 1.60 A; A=1-204.
DR PDB; 2RIU; X-ray; 1.70 A; A=1-204.
DR PDBsum; 1TKS; -.
DR PDBsum; 1TKU; -.
DR PDBsum; 2RIS; -.
DR PDBsum; 2RIU; -.
DR AlphaFoldDB; Q5A3V6; -.
DR SMR; Q5A3V6; -.
DR BioGRID; 1225049; 1.
DR STRING; 237561.Q5A3V6; -.
DR GeneID; 3642062; -.
DR KEGG; cal:CAALFM_C112360CA; -.
DR CGD; CAL0000192139; RIB3.
DR eggNOG; KOG1284; Eukaryota.
DR HOGENOM; CLU_020273_3_0_1; -.
DR InParanoid; Q5A3V6; -.
DR OrthoDB; 1382176at2759; -.
DR BRENDA; 4.1.99.12; 1096.
DR SABIO-RK; Q5A3V6; -.
DR UniPathway; UPA00275; UER00399.
DR EvolutionaryTrace; Q5A3V6; -.
DR PRO; PR:Q5A3V6; -.
DR Proteomes; UP000000559; Chromosome 1.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005758; C:mitochondrial intermembrane space; IBA:GO_Central.
DR GO; GO:0008686; F:3,4-dihydroxy-2-butanone-4-phosphate synthase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009060; P:aerobic respiration; IBA:GO_Central.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IBA:GO_Central.
DR HAMAP; MF_00180; RibB; 1.
DR InterPro; IPR017945; DHBP_synth_RibB-like_a/b_dom.
DR InterPro; IPR000422; DHBP_synthase_RibB.
DR Pfam; PF00926; DHBP_synthase; 1.
DR SUPFAM; SSF55821; SSF55821; 1.
DR TIGRFAMs; TIGR00506; ribB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Glutathionylation; Lyase;
KW Magnesium; Manganese; Metal-binding; Reference proteome;
KW Riboflavin biosynthesis.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:15328619"
FT CHAIN 2..204
FT /note="3,4-dihydroxy-2-butanone 4-phosphate synthase"
FT /id="PRO_0000296685"
FT BINDING 30
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q8TG90"
FT BINDING 30
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q8TG90"
FT BINDING 34
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000269|PubMed:15328619,
FT ECO:0007744|PDB:1TKU, ECO:0007744|PDB:2RIU"
FT BINDING 85
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000269|PubMed:15328619,
FT ECO:0007744|PDB:1TKU, ECO:0007744|PDB:2RIU"
FT BINDING 142..146
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000269|PubMed:15328619,
FT ECO:0007744|PDB:1TKU, ECO:0007744|PDB:2RIU"
FT BINDING 145
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q8TG90"
FT SITE 128
FT /note="Essential for catalytic activity"
FT /evidence="ECO:0000250"
FT SITE 166
FT /note="Essential for catalytic activity"
FT /evidence="ECO:0000305|PubMed:15328619"
FT MOD_RES 59
FT /note="S-glutathionyl cysteine"
FT /evidence="ECO:0000250|UniProtKB:Q99258"
FT MUTAGEN 59
FT /note="C->A: Increases Km for substrate 18-fold. Reduces
FT activity by 30%."
FT MUTAGEN 87
FT /note="Y->A: Increases Km for substrate 4-fold. Reduces
FT activity by 98%."
FT /evidence="ECO:0000269|PubMed:15328619"
FT MUTAGEN 92
FT /note="D->A: Loss of activity. Alters protein folding and
FT stability."
FT /evidence="ECO:0000269|PubMed:15328619"
FT MUTAGEN 166
FT /note="E->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:15328619"
FT CONFLICT 183
FT /note="Q -> R (in Ref. 4)"
FT /evidence="ECO:0000305"
FT HELIX 8..16
FT /evidence="ECO:0007829|PDB:1TKS"
FT STRAND 21..27
FT /evidence="ECO:0007829|PDB:1TKS"
FT STRAND 34..38
FT /evidence="ECO:0007829|PDB:1TKS"
FT HELIX 39..41
FT /evidence="ECO:0007829|PDB:1TKS"
FT HELIX 44..52
FT /evidence="ECO:0007829|PDB:1TKS"
FT STRAND 59..63
FT /evidence="ECO:0007829|PDB:1TKS"
FT HELIX 64..69
FT /evidence="ECO:0007829|PDB:1TKS"
FT STRAND 91..94
FT /evidence="ECO:0007829|PDB:1TKS"
FT STRAND 98..100
FT /evidence="ECO:0007829|PDB:1TKS"
FT HELIX 103..114
FT /evidence="ECO:0007829|PDB:1TKS"
FT HELIX 120..122
FT /evidence="ECO:0007829|PDB:1TKS"
FT STRAND 123..134
FT /evidence="ECO:0007829|PDB:1TKS"
FT HELIX 138..140
FT /evidence="ECO:0007829|PDB:1TKS"
FT HELIX 145..155
FT /evidence="ECO:0007829|PDB:1TKS"
FT STRAND 160..168
FT /evidence="ECO:0007829|PDB:1TKS"
FT TURN 170..172
FT /evidence="ECO:0007829|PDB:1TKS"
FT HELIX 178..188
FT /evidence="ECO:0007829|PDB:1TKS"
FT STRAND 192..194
FT /evidence="ECO:0007829|PDB:1TKS"
FT HELIX 195..202
FT /evidence="ECO:0007829|PDB:1TKS"
SQ SEQUENCE 204 AA; 22658 MW; 5FEC62C3ABDA822E CRC64;
MTNIFTPIEE ALEAYKNGEF LIVMDDEDRE NEGDLIMAAE LITQEKMAFL VRYSSGYVCV
PLSEERANQL ELPPMLANRS DRHGTAYTIT CDFAEGTTTG ISAHDRALTT RSLANPNSKP
QDFIKPGHIL PLRAVPGLLK KRRGHTEAAV QLSTLAGLQP AGVICELVRD EDGLMMRLDD
CIQFGKKHGI KIININQLVE YISK
