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   13-SEP-2023, entry version 109.
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   eggNOG; KOG1284; Eukaryota.
DR   HOGENOM; CLU_020273_3_0_1; -.
DR   InParanoid; Q5A3V6; -.
DR   OrthoDB; 5489599at2759; -.
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:0008686; F:3,4-dihydroxy-2-butanone-4-phosphate synthase activity; IEA:UniProtKB-EC.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0009231; P:riboflavin biosynthetic process; IEA:UniProtKB-UniPathway.
DR   Gene3D; 3.90.870.10; DHBP synthase; 1.
DR   HAMAP; MF_00180; RibB; 1.
DR   InterPro; IPR017945; DHBP_synth_RibB-like_a/b_dom.
DR   InterPro; IPR000422; DHBP_synthase_RibB.
DR   NCBIfam; TIGR00506; ribB; 1.
DR   PANTHER; PTHR21327:SF18; 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE; 1.
DR   PANTHER; PTHR21327; GTP CYCLOHYDROLASE II-RELATED; 1.
DR   Pfam; PF00926; DHBP_synthase; 1.
DR   SUPFAM; SSF55821; YrdC/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
//