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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.
11-DEC-2019, entry version 102.
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; -.
HOGENOM; HOG000115442; -.
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; Reference proteome; 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)]
[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 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)]
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[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)]
[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)]
[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 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 ribH DMD85_09030] 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 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)]
[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 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 DI032_08595 DI051_08635 DI125_01930 DI126_02025 DI127_02025 DI129_04455 DI130_01930 DIZ51_08590 DIZ69_08590] 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 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)]
[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)]
[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 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)]
[hchA A8C65_13880 A9R57_25255 AKG99_20940 AMK83_16550 B7C53_22525 B9M99_11580 B9T59_01945 BJJ90_15205 BMT49_12710 BON66_15955 BON86_06490 BON95_14610 BUE81_10670 BvCms12BK_01457 BvCms28BK_04168 BvCmsHHP001_02632 BvCmsKKP061_00566 BvCmsKSP015_01352 BvCmsKSP045_04450 BvCmsKSP058_03204 BvCmsKSP067_02879 BvCmsKSP083_03900 BvCmsNSP006_03750 BvCmsNSP007_03329 BvCmsNSP047_03567 BvCmsSINP011_04162 BW690_17225 BZL69_29425 C2U48_24800 C5715_19445 C5N07_21380 C6669_19295 C7B06_02290 C7B07_03930 C9025_17620 C9077_19550 C9078_12950 C9083_21590 C9212_13125 C9Y80_10480 C9Y95_17520 C9Z12_18550 CDC27_10055 CDL37_00765 CI694_25210 CIJ94_05515 COD46_23180 CQP61_17160 CRD98_26150 D2188_01360 D6W60_25270 D9D20_21030 D9D43_06110 D9H68_20750 D9H70_25730 D9I87_15275 DEN89_24995 DEO04_05510 DL800_09215 DNQ41_14245 DQE83_22775 DTL43_21780 DTM25_06080 DU321_04440 DXT73_20690 E2134_24005 E2135_17195 E2855_02503 E2863_02392 E5P22_21380 E5S46_06650 EB575_25290 EC95NR1_00961 ED648_25045 ELT20_21515 ELV08_24970 EPS97_16570 EPT01_11070 EQ825_23250 ERS085379_01273 ERS085386_05041 ExPECSC038_01920 EXX71_02385 EXX78_21815 EYD11_09165 FNJ83_13175 FQ915_04255 FQR64_09390 FWK02_18105 HmCmsJML079_02678 HMPREF3040_01583 HW43_13705 NCTC10082_04431 NCTC10418_03071 NCTC10767_03558 NCTC11022_01867 NCTC11126_04427 NCTC11181_05650 NCTC12950_02263 NCTC8985_00529 NCTC9111_05933 NCTC9703_00277 PGD_01271 PU06_24500 SAMEA3472043_00447 SAMEA3472055_03589 SAMEA3472056_01268 SAMEA3472070_00654 SAMEA3472080_04213 SAMEA3472090_03376 SAMEA3472110_00060 SAMEA3472112_00448 SAMEA3752372_00752 UN91_23615 WQ89_10695] Protein/nucleic acid deglycase HchA (EC 3.1.2.-) (EC 3.5.1.-) (EC 3.5.1.124) (Maillard deglycase)
[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)]
[ribA ribBA BTZ20_2732] 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)]

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