RIBXA_VIBVY
ID RIBXA_VIBVY Reviewed; 367 AA.
AC Q7MGG3;
DT 16-SEP-2015, integrated into UniProtKB/Swiss-Prot.
DT 15-DEC-2003, sequence version 1.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=Riboflavin biosynthesis protein VVA0006 {ECO:0000305};
DE Includes:
DE RecName: Full=Riboflavin biosynthesis intermediates N-glycosidase {ECO:0000305|PubMed:25431972};
DE EC=3.2.2.- {ECO:0000269|PubMed:25431972};
DE Includes:
DE RecName: Full=GTP cyclohydrolase-2;
DE EC=3.5.4.25 {ECO:0000269|PubMed:25431972};
DE AltName: Full=GTP cyclohydrolase II {ECO:0000303|PubMed:25431972};
GN OrderedLocusNames=VVA0006 {ECO:0000312|EMBL:BAC96032.1};
OS Vibrio vulnificus (strain YJ016).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=196600;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=YJ016;
RX PubMed=14656965; DOI=10.1101/gr.1295503;
RA Chen C.-Y., Wu K.-M., Chang Y.-C., Chang C.-H., Tsai H.-C., Liao T.-L.,
RA Liu Y.-M., Chen H.-J., Shen A.B.-T., Li J.-C., Su T.-L., Shao C.-P.,
RA Lee C.-T., Hor L.-I., Tsai S.-F.;
RT "Comparative genome analysis of Vibrio vulnificus, a marine pathogen.";
RL Genome Res. 13:2577-2587(2003).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND PATHWAY.
RX PubMed=25431972; DOI=10.1042/bj20141237;
RA Frelin O., Huang L., Hasnain G., Jeffryes J.G., Ziemak M.J., Rocca J.R.,
RA Wang B., Rice J., Roje S., Yurgel S.N., Gregory J.F. III, Edison A.S.,
RA Henry C.S., de Crecy-Lagard V., Hanson A.D.;
RT "A directed-overflow and damage-control N-glycosidase in riboflavin
RT biosynthesis.";
RL Biochem. J. 466:137-145(2015).
CC -!- FUNCTION: Catalyzes the hydrolysis of the N-glycosidic bond in the
CC first two intermediates of riboflavin biosynthesis, which are highly
CC reactive metabolites, yielding relatively innocuous products. Thus, can
CC divert a surplus of harmful intermediates into relatively harmless
CC products and pre-empt the damage these intermediates would otherwise
CC do. Has no activity against GTP, nucleoside monophosphates or ADP-
CC ribose. {ECO:0000269|PubMed:25431972}.
CC -!- FUNCTION: Catalyzes the conversion of GTP to 2,5-diamino-6-
CC ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and
CC pyrophosphate. {ECO:0000269|PubMed:25431972}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine +
CC H2O = 2,5,6-triamino-4-hydroxypyrimidine + D-ribose 5-phosphate;
CC Xref=Rhea:RHEA:23436, ChEBI:CHEBI:15377, ChEBI:CHEBI:58614,
CC ChEBI:CHEBI:78346, ChEBI:CHEBI:137796;
CC Evidence={ECO:0000269|PubMed:25431972};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-amino-6-(5-phospho-D-ribosylamino)uracil + H2O = 5,6-
CC diaminouracil + D-ribose 5-phosphate; Xref=Rhea:RHEA:55020,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:46252, ChEBI:CHEBI:58453,
CC ChEBI:CHEBI:78346; Evidence={ECO:0000269|PubMed:25431972};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=GTP + 4 H2O = 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-
CC pyrimidine + formate + 3 H(+) + 2 phosphate; Xref=Rhea:RHEA:23704,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:15740,
CC ChEBI:CHEBI:37565, ChEBI:CHEBI:43474, ChEBI:CHEBI:58614; EC=3.5.4.25;
CC Evidence={ECO:0000269|PubMed:25431972};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:P0A7I7};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000250|UniProtKB:P0A7I7};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.45 mM for 2,5-diamino-6-hydroxy-4-(5-phospho-D-
CC ribosylamino)pyrimidine {ECO:0000269|PubMed:25431972};
CC KM=0.51 mM for 5-amino-6-(5-phospho-D-ribosylamino)uracil
CC {ECO:0000269|PubMed:25431972};
CC Note=kcat is 137 sec(-1) with 2,5-diamino-6-hydroxy-4-(5-phospho-D-
CC ribosylamino)pyrimidine as substrate. kcat is 0.07 sec(-1) with 5-
CC amino-6-(5-phospho-D-ribosylamino)uracil as substrate.
CC {ECO:0000269|PubMed:25431972};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 1/4. {ECO:0000305|PubMed:25431972}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the YbiA family.
CC {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the GTP
CC cyclohydrolase II family. {ECO:0000305}.
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DR EMBL; BA000038; BAC96032.1; -; Genomic_DNA.
DR AlphaFoldDB; Q7MGG3; -.
DR SMR; Q7MGG3; -.
DR STRING; 672.VV93_v1c30170; -.
DR EnsemblBacteria; BAC96032; BAC96032; BAC96032.
DR KEGG; vvy:VVA0006; -.
DR eggNOG; COG0807; Bacteria.
DR eggNOG; COG3236; Bacteria.
DR HOGENOM; CLU_020273_2_1_6; -.
DR OMA; MRDYAFC; -.
DR UniPathway; UPA00275; UER00400.
DR Proteomes; UP000002675; Chromosome II.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0003935; F:GTP cyclohydrolase II activity; IGI:UniProtKB.
DR GO; GO:0016799; F:hydrolase activity, hydrolyzing N-glycosyl compounds; IDA:UniProtKB.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:1901135; P:carbohydrate derivative metabolic process; IDA:UniProtKB.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IGI:UniProtKB.
DR CDD; cd00641; GTP_cyclohydro2; 1.
DR CDD; cd15457; NADAR; 1.
DR Gene3D; 1.10.357.40; -; 1.
DR Gene3D; 3.40.50.10990; -; 1.
DR HAMAP; MF_00179; RibA; 1.
DR InterPro; IPR032677; GTP_cyclohydro_II.
DR InterPro; IPR012816; NADAR.
DR InterPro; IPR000926; RibA.
DR InterPro; IPR036144; RibA-like_sf.
DR InterPro; IPR037238; YbiA-like_sf.
DR Pfam; PF00925; GTP_cyclohydro2; 1.
DR Pfam; PF08719; NADAR; 1.
DR SUPFAM; SSF142695; SSF142695; 1.
DR SUPFAM; SSF143990; SSF143990; 1.
DR TIGRFAMs; TIGR00505; ribA; 1.
DR TIGRFAMs; TIGR02464; ribofla_fusion; 1.
PE 1: Evidence at protein level;
KW Glycosidase; GTP-binding; Hydrolase; Metal-binding; Multifunctional enzyme;
KW Nucleotide-binding; Reference proteome; Riboflavin biosynthesis; Zinc.
FT CHAIN 1..367
FT /note="Riboflavin biosynthesis protein VVA0006"
FT /id="PRO_0000433624"
FT ACT_SITE 292
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P0A7I7"
FT ACT_SITE 294
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:P0A7I7"
FT BINDING 215..219
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250|UniProtKB:P0A7I7"
FT BINDING 220
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P0A7I7"
FT BINDING 231
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P0A7I7"
FT BINDING 233
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P0A7I7"
FT BINDING 236
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250|UniProtKB:P0A7I7"
FT BINDING 258..260
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250|UniProtKB:P0A7I7"
FT BINDING 280
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250|UniProtKB:P0A7I7"
FT BINDING 315
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250|UniProtKB:P0A7I7"
FT BINDING 320
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250|UniProtKB:P0A7I7"
SQ 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
