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Riboflavin biosynthesis protein VVA0006 [Includes: Riboflavin biosynthesis intermediates N-glycosidase (EC 3.2.2.-); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]

 RIBXA_VIBVY             Reviewed;         367 AA.
Q7MGG3;
16-SEP-2015, integrated into UniProtKB/Swiss-Prot.
15-DEC-2003, sequence version 1.
12-AUG-2020, entry version 106.
RecName: Full=Riboflavin biosynthesis protein VVA0006 {ECO:0000305};
Includes:
RecName: Full=Riboflavin biosynthesis intermediates N-glycosidase {ECO:0000305|PubMed:25431972};
EC=3.2.2.- {ECO:0000269|PubMed:25431972};
Includes:
RecName: Full=GTP cyclohydrolase-2;
EC=3.5.4.25 {ECO:0000269|PubMed:25431972};
AltName: Full=GTP cyclohydrolase II {ECO:0000303|PubMed:25431972};
OrderedLocusNames=VVA0006 {ECO:0000312|EMBL:BAC96032.1};
Vibrio vulnificus (strain YJ016).
Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
Vibrio.
NCBI_TaxID=196600;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=YJ016;
PubMed=14656965; DOI=10.1101/gr.1295503;
Chen C.-Y., Wu K.-M., Chang Y.-C., Chang C.-H., Tsai H.-C., Liao T.-L.,
Liu Y.-M., Chen H.-J., Shen A.B.-T., Li J.-C., Su T.-L., Shao C.-P.,
Lee C.-T., Hor L.-I., Tsai S.-F.;
"Comparative genome analysis of Vibrio vulnificus, a marine pathogen.";
Genome Res. 13:2577-2587(2003).
[2]
FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL
PROPERTIES, AND PATHWAY.
PubMed=25431972; DOI=10.1042/bj20141237;
Frelin O., Huang L., Hasnain G., Jeffryes J.G., Ziemak M.J., Rocca J.R.,
Wang B., Rice J., Roje S., Yurgel S.N., Gregory J.F. III, Edison A.S.,
Henry C.S., de Crecy-Lagard V., Hanson A.D.;
"A directed-overflow and damage-control N-glycosidase in riboflavin
biosynthesis.";
Biochem. J. 466:137-145(2015).
-!- FUNCTION: Catalyzes the hydrolysis of the N-glycosidic bond in the
first two intermediates of riboflavin biosynthesis, which are highly
reactive metabolites, yielding relatively innocuous products. Thus, can
divert a surplus of harmful intermediates into relatively harmless
products and pre-empt the damage these intermediates would otherwise
do. Has no activity against GTP, nucleoside monophosphates or ADP-
ribose. {ECO:0000269|PubMed:25431972}.
-!- FUNCTION: Catalyzes the conversion of GTP to 2,5-diamino-6-
ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and
pyrophosphate. {ECO:0000269|PubMed:25431972}.
-!- CATALYTIC ACTIVITY:
Reaction=2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine +
H2O = 2,5,6-triamino-4-hydroxypyrimidine + D-ribose 5-phosphate;
Xref=Rhea:RHEA:23436, ChEBI:CHEBI:15377, ChEBI:CHEBI:58614,
ChEBI:CHEBI:78346, ChEBI:CHEBI:137796;
Evidence={ECO:0000269|PubMed:25431972};
-!- CATALYTIC ACTIVITY:
Reaction=5-amino-6-(5-phospho-D-ribosylamino)uracil + H2O = 5,6-
diaminouracil + D-ribose 5-phosphate; Xref=Rhea:RHEA:55020,
ChEBI:CHEBI:15377, ChEBI:CHEBI:46252, ChEBI:CHEBI:58453,
ChEBI:CHEBI:78346; Evidence={ECO:0000269|PubMed:25431972};
-!- CATALYTIC ACTIVITY:
Reaction=GTP + 3 H2O = 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-
pyrimidine + diphosphate + formate + 2 H(+); Xref=Rhea:RHEA:23704,
ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:15740,
ChEBI:CHEBI:33019, ChEBI:CHEBI:37565, ChEBI:CHEBI:58614; EC=3.5.4.25;
Evidence={ECO:0000269|PubMed:25431972};
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000250|UniProtKB:P0A7I7};
Note=Binds 1 zinc ion per subunit. {ECO:0000250|UniProtKB:P0A7I7};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.45 mM for 2,5-diamino-6-hydroxy-4-(5-phospho-D-
ribosylamino)pyrimidine {ECO:0000269|PubMed:25431972};
KM=0.51 mM for 5-amino-6-(5-phospho-D-ribosylamino)uracil
{ECO:0000269|PubMed:25431972};
Note=kcat is 137 sec(-1) with 2,5-diamino-6-hydroxy-4-(5-phospho-D-
ribosylamino)pyrimidine as substrate. kcat is 0.07 sec(-1) with 5-
amino-6-(5-phospho-D-ribosylamino)uracil as substrate.
{ECO:0000269|PubMed:25431972};
-!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
ribitylamino)uracil from GTP: step 1/4. {ECO:0000305|PubMed:25431972}.
-!- SIMILARITY: In the N-terminal section; belongs to the YbiA family.
{ECO:0000305}.
-!- SIMILARITY: In the C-terminal section; belongs to the GTP
cyclohydrolase II family. {ECO:0000305}.
---------------------------------------------------------------------------
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EMBL; BA000038; BAC96032.1; -; Genomic_DNA.
SMR; Q7MGG3; -.
STRING; 672.VV93_v1c30170; -.
EnsemblBacteria; BAC96032; BAC96032; BAC96032.
KEGG; vvy:VVA0006; -.
eggNOG; COG0807; Bacteria.
eggNOG; COG3236; Bacteria.
HOGENOM; CLU_020273_2_1_6; -.
KO; K01497; -.
OMA; MRDYAFC; -.
BioCyc; VVUL196600:GJ9W-3392-MONOMER; -.
UniPathway; UPA00275; UER00400.
Proteomes; UP000002675; Chromosome II.
GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
GO; GO:0003935; F:GTP cyclohydrolase II activity; IGI:UniProtKB.
GO; GO:0016799; F:hydrolase activity, hydrolyzing N-glycosyl compounds; IDA:UniProtKB.
GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
GO; GO:1901135; P:carbohydrate derivative metabolic process; IDA:UniProtKB.
GO; GO:0009231; P:riboflavin biosynthetic process; IGI:UniProtKB.
CDD; cd00641; GTP_cyclohydro2; 1.
CDD; cd15457; NADAR; 1.
Gene3D; 1.10.357.40; -; 1.
Gene3D; 3.40.50.10990; -; 1.
HAMAP; MF_00179; RibA; 1.
InterPro; IPR032677; GTP_cyclohydro_II.
InterPro; IPR012816; NADAR.
InterPro; IPR000926; RibA.
InterPro; IPR036144; RibA-like_sf.
InterPro; IPR037238; YbiA-like_sf.
Pfam; PF08719; DUF1768; 1.
Pfam; PF00925; GTP_cyclohydro2; 1.
SUPFAM; SSF142695; SSF142695; 1.
SUPFAM; SSF143990; SSF143990; 1.
TIGRFAMs; TIGR00505; ribA; 1.
TIGRFAMs; TIGR02464; ribofla_fusion; 1.
1: Evidence at protein level;
Glycosidase; GTP-binding; Hydrolase; Metal-binding; Multifunctional enzyme;
Nucleotide-binding; Riboflavin biosynthesis; Zinc.
CHAIN 1..367
/note="Riboflavin biosynthesis protein VVA0006"
/id="PRO_0000433624"
NP_BIND 215..219
/note="GTP"
/evidence="ECO:0000250|UniProtKB:P0A7I7"
NP_BIND 258..260
/note="GTP"
/evidence="ECO:0000250|UniProtKB:P0A7I7"
ACT_SITE 292
/note="Proton acceptor"
/evidence="ECO:0000250|UniProtKB:P0A7I7"
ACT_SITE 294
/note="Nucleophile"
/evidence="ECO:0000250|UniProtKB:P0A7I7"
METAL 220
/note="Zinc; catalytic"
/evidence="ECO:0000250|UniProtKB:P0A7I7"
METAL 231
/note="Zinc; catalytic"
/evidence="ECO:0000250|UniProtKB:P0A7I7"
METAL 233
/note="Zinc; catalytic"
/evidence="ECO:0000250|UniProtKB:P0A7I7"
BINDING 236
/note="GTP"
/evidence="ECO:0000250|UniProtKB:P0A7I7"
BINDING 280
/note="GTP"
/evidence="ECO:0000250|UniProtKB:P0A7I7"
BINDING 315
/note="GTP"
/evidence="ECO:0000250|UniProtKB:P0A7I7"
BINDING 320
/note="GTP"
/evidence="ECO:0000250|UniProtKB:P0A7I7"
SEQUENCE 367 AA; 42270 MW; 5C895A2EAFD085BF CRC64;
MHFVSYSLCY DVRSNIMEQP IYFYEPDENH GFLANFYPCS ITVSGTCWPS SEHYYQAQKF
DDVRLQEKVL RAEDAAQAFR LSREYQQWQR HDWYDIRVEV MRFIVREKFL QNTPLAHQLL
ATGDTELKEH SHKDAFWGDG GDGHGRNELG RILMMVREEL QEHAPYNLVQ FIDSAKLPTQ
WGTFQMYGFI EKATGKEHLA LVYGDIEQQA APLIRLHSEC LTGDALFSAR CDCGFQLAKA
LQNIVAEGAG VLLYLRQEGR GIGLINKIRA YHLQDDGADT VEANEQLGFG ADMRDYAFCR
GILSFLGIER VRLMTNNPRK VKALQLANIE VTERVPLQEG NNPHNHQYLR TKADKLGHMF
DRNFVKP


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Related Genes :
[VVA0006] Riboflavin biosynthesis protein VVA0006 [Includes: Riboflavin biosynthesis intermediates N-glycosidase (EC 3.2.2.-); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[RIBA1 RIBBA At5g64300 MSJ1.14] Bifunctional riboflavin biosynthesis protein RIBA 1, chloroplastic (AtRIBA1) [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA ribA MW1709] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA APL_0384] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[PYRR PHS1 At3g47390 T21L8.140] Riboflavin biosynthesis protein PYRR, chloroplastic [Includes: Inactive diaminohydroxyphosphoribosylaminopyrimidine deaminase (DRAP deaminase) (Riboflavin-specific deaminase); 5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193) (HTP reductase); Riboflavin biosynthesis intermediates N-glycosidase (EC 3.2.2.-)]
[PYRR GRMZM2G090068] Riboflavin biosynthesis protein PYRR, chloroplastic [Includes: Inactive diaminohydroxyphosphoribosylaminopyrimidine deaminase (DRAP deaminase) (Riboflavin-specific deaminase); 5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193) (HTP reductase); Riboflavin biosynthesis intermediates N-glycosidase (EC 3.2.2.-)]
[ribBA ribA ribA2 Rv1415 MTCY21B4.33] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA ribA/ribB CT_731] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA ribA sll1894] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA BCG_1476] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA ribA aq_350] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA Paes_0583] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA BCG9842_B1015] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[RIBA2 At2g22450 F14M13.15] Monofunctional riboflavin biosynthesis protein RIBA 2, chloroplastic [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); Inactive GTP cyclohydrolase-2 (GTP cyclohydrolase II)]
[ribBA ribA SA1587] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA APJL_0404] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA ribA BSU23260] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA CHU_0931] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribH ribBA E6H97_11685] Multifunctional fusion protein [Includes: Riboflavin biosynthesis protein RibBA; 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II); 6,7-dimethyl-8-ribityllumazine synthase (DMRL synthase) (LS) (Lumazine synthase) (EC 2.5.1.78)]
[ribBA ribH GA0115236_158411] Multifunctional fusion protein [Includes: Riboflavin biosynthesis protein RibBA; 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II); 6,7-dimethyl-8-ribityllumazine synthase (DMRL synthase) (LS) (Lumazine synthase) (EC 2.5.1.78)]
[ribBA PGN_0643] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA Teth39_0023] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA BCA_4224] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA ribA ribA2 MT1458] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA ribA] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA RER_30220] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA BcerKBAB4_3943] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA BT_2416] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA ribA/ribB CPn_0872 CP_0997 CpB0901] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]
[ribBA ribA/B TC_0104] Riboflavin biosynthesis protein RibBA [Includes: 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12); GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II)]

Bibliography :