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Riboflavin biosynthesis protein RibBA [Includes: GTP cyclohydrolase-2 (EC 3.5.4.25) (GTP cyclohydrolase II); 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12)]
A0A0A8WQV6_9DELT Unreviewed; 401 AA.
A0A0A8WQV6;
04-MAR-2015, integrated into UniProtKB/TrEMBL.
04-MAR-2015, sequence version 1.
16-JAN-2019, entry version 36.
RecName: Full=Riboflavin biosynthesis protein RibBA {ECO:0000256|HAMAP-Rule:MF_01283};
Includes:
RecName: Full=3,4-dihydroxy-2-butanone 4-phosphate synthase {ECO:0000256|HAMAP-Rule:MF_01283};
Short=DHBP synthase {ECO:0000256|HAMAP-Rule:MF_01283};
EC=4.1.99.12 {ECO:0000256|HAMAP-Rule:MF_01283};
Includes:
RecName: Full=GTP cyclohydrolase-2 {ECO:0000256|HAMAP-Rule:MF_01283};
EC=3.5.4.25 {ECO:0000256|HAMAP-Rule:MF_01283};
AltName: Full=GTP cyclohydrolase II {ECO:0000256|HAMAP-Rule:MF_01283};
Name=ribBA {ECO:0000256|HAMAP-Rule:MF_01283,
ECO:0000313|EMBL:GAM10030.1};
ORFNames=OR1_02316 {ECO:0000313|EMBL:GAM10030.1};
Geobacter sp. OR-1.
Bacteria; Proteobacteria; Deltaproteobacteria; Desulfuromonadales;
Geobacteraceae; Geobacter.
NCBI_TaxID=1266765 {ECO:0000313|EMBL:GAM10030.1, ECO:0000313|Proteomes:UP000030972};
[1] {ECO:0000313|EMBL:GAM10030.1, ECO:0000313|Proteomes:UP000030972}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=OR-1 {ECO:0000313|EMBL:GAM10030.1,
ECO:0000313|Proteomes:UP000030972};
PubMed=23668621; DOI=10.1021/es400231x;
Ohtsuka T., Yamaguchi N., Makino T., Sakurai K., Kimura K., Kudo K.,
Homma E., Dong DT., Amachi S.;
"Arsenic dissolution from Japanese paddy soil by a dissimilatory
arsenate-reducing bacterium Geobacter sp. OR-1.";
Environ. Sci. Technol. 47:6263-6271(2013).
[2] {ECO:0000313|EMBL:GAM10030.1, ECO:0000313|Proteomes:UP000030972}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=OR-1 {ECO:0000313|EMBL:GAM10030.1,
ECO:0000313|Proteomes:UP000030972};
Ehara A., Suzuki H., Amachi S.;
"Draft Genome Sequence of Geobacter sp. Strain OR-1, an Arsenate-
Respiring Bacterium Isolated from Japanese Paddy Soil.";
Genome Announc. 3:e01478-14(2015).
-!- FUNCTION: Catalyzes the conversion of D-ribulose 5-phosphate to
formate and 3,4-dihydroxy-2-butanone 4-phosphate.
{ECO:0000256|HAMAP-Rule:MF_01283, ECO:0000256|SAAS:SAAS00739193}.
-!- FUNCTION: Catalyzes the conversion of GTP to 2,5-diamino-6-
ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and
pyrophosphate. {ECO:0000256|HAMAP-Rule:MF_01283}.
-!- CATALYTIC ACTIVITY:
Reaction=D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl
phosphate + formate + H(+); Xref=Rhea:RHEA:18457,
ChEBI:CHEBI:15378, ChEBI:CHEBI:15740, ChEBI:CHEBI:58121,
ChEBI:CHEBI:58830; EC=4.1.99.12; Evidence={ECO:0000256|HAMAP-
Rule:MF_01283};
-!- 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:0000256|HAMAP-Rule:MF_01283,
ECO:0000256|SAAS:SAAS01116086};
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000256|HAMAP-Rule:MF_01283};
Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
Evidence={ECO:0000256|HAMAP-Rule:MF_01283};
Note=Binds 2 divalent metal cations per subunit. Magnesium or
manganese. {ECO:0000256|HAMAP-Rule:MF_01283};
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000256|HAMAP-Rule:MF_01283};
Note=Binds 1 zinc ion per subunit. {ECO:0000256|HAMAP-
Rule:MF_01283};
-!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 2-
hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate: step
1/1. {ECO:0000256|HAMAP-Rule:MF_01283}.
-!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-
6-(D-ribitylamino)uracil from GTP: step 1/4. {ECO:0000256|HAMAP-
Rule:MF_01283, ECO:0000256|SAAS:SAAS00711724}.
-!- SIMILARITY: In the C-terminal section; belongs to the GTP
cyclohydrolase II family. {ECO:0000256|HAMAP-Rule:MF_01283,
ECO:0000256|SAAS:SAAS00789992}.
-!- SIMILARITY: In the N-terminal section; belongs to the DHBP
synthase family. {ECO:0000256|HAMAP-Rule:MF_01283,
ECO:0000256|SAAS:SAAS00534513}.
-!- CAUTION: Lacks conserved residue(s) required for the propagation
of feature annotation. {ECO:0000256|HAMAP-Rule:MF_01283}.
-!- CAUTION: The sequence shown here is derived from an
EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is
preliminary data. {ECO:0000313|EMBL:GAM10030.1}.
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EMBL; BAZF01000009; GAM10030.1; -; Genomic_DNA.
RefSeq; WP_041971966.1; NZ_BAZF01000009.1.
EnsemblBacteria; GAM10030; GAM10030; OR1_02316.
OrthoDB; 900513at2; -.
UniPathway; UPA00275; UER00399.
UniPathway; UPA00275; UER00400.
Proteomes; UP000030972; Unassembled WGS sequence.
GO; GO:0008686; F:3,4-dihydroxy-2-butanone-4-phosphate synthase activity; IEA:UniProtKB-UniRule.
GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
GO; GO:0003935; F:GTP cyclohydrolase II activity; IEA:UniProtKB-UniRule.
GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
GO; GO:0030145; F:manganese ion binding; IEA:UniProtKB-UniRule.
GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
GO; GO:0009231; P:riboflavin biosynthetic process; IEA:UniProtKB-UniRule.
CDD; cd00641; GTP_cyclohydro2; 1.
Gene3D; 3.40.50.10990; -; 1.
HAMAP; MF_00179; RibA; 1.
HAMAP; MF_00180; RibB; 1.
HAMAP; MF_01283; RibBA; 1.
InterPro; IPR017945; DHBP_synth_RibB-like_a/b_dom.
InterPro; IPR000422; DHBP_synthase_RibB.
InterPro; IPR032677; GTP_cyclohydro_II.
InterPro; IPR000926; RibA.
InterPro; IPR036144; RibA-like_sf.
InterPro; IPR016299; Riboflavin_synth_RibBA.
Pfam; PF00926; DHBP_synthase; 1.
Pfam; PF00925; GTP_cyclohydro2; 1.
SUPFAM; SSF142695; SSF142695; 1.
SUPFAM; SSF55821; SSF55821; 1.
TIGRFAMs; TIGR00505; ribA; 1.
TIGRFAMs; TIGR00506; ribB; 1.
3: Inferred from homology;
Complete proteome {ECO:0000313|Proteomes:UP000030972};
GTP-binding {ECO:0000256|HAMAP-Rule:MF_01283,
ECO:0000256|SAAS:SAAS00711691};
Hydrolase {ECO:0000256|HAMAP-Rule:MF_01283,
ECO:0000256|SAAS:SAAS01033620};
Lyase {ECO:0000256|HAMAP-Rule:MF_01283};
Magnesium {ECO:0000256|HAMAP-Rule:MF_01283};
Manganese {ECO:0000256|HAMAP-Rule:MF_01283};
Metal-binding {ECO:0000256|HAMAP-Rule:MF_01283,
ECO:0000256|SAAS:SAAS00037896};
Multifunctional enzyme {ECO:0000256|HAMAP-Rule:MF_01283};
Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_01283,
ECO:0000256|SAAS:SAAS00711691};
Reference proteome {ECO:0000313|Proteomes:UP000030972};
Riboflavin biosynthesis {ECO:0000256|HAMAP-Rule:MF_01283,
ECO:0000256|SAAS:SAAS00037880};
Zinc {ECO:0000256|HAMAP-Rule:MF_01283, ECO:0000256|SAAS:SAAS00711685}.
DOMAIN 208 373 GTP_cyclohydro2.
{ECO:0000259|Pfam:PF00925}.
NP_BIND 253 257 GTP. {ECO:0000256|HAMAP-Rule:MF_01283}.
NP_BIND 296 298 GTP. {ECO:0000256|HAMAP-Rule:MF_01283}.
REGION 1 201 DHBP synthase. {ECO:0000256|HAMAP-
Rule:MF_01283}.
REGION 27 28 D-ribulose 5-phosphate binding.
{ECO:0000256|HAMAP-Rule:MF_01283}.
REGION 202 401 GTP cyclohydrolase II.
{ECO:0000256|HAMAP-Rule:MF_01283}.
ACT_SITE 330 330 Proton acceptor; for GTP cyclohydrolase
activity. {ECO:0000256|HAMAP-
Rule:MF_01283}.
ACT_SITE 332 332 Nucleophile; for GTP cyclohydrolase
activity. {ECO:0000256|HAMAP-
Rule:MF_01283}.
METAL 28 28 Magnesium or manganese 1.
{ECO:0000256|HAMAP-Rule:MF_01283}.
METAL 28 28 Magnesium or manganese 2.
{ECO:0000256|HAMAP-Rule:MF_01283}.
METAL 258 258 Zinc; catalytic. {ECO:0000256|HAMAP-
Rule:MF_01283}.
METAL 269 269 Zinc; catalytic. {ECO:0000256|HAMAP-
Rule:MF_01283}.
METAL 271 271 Zinc; catalytic. {ECO:0000256|HAMAP-
Rule:MF_01283}.
BINDING 32 32 D-ribulose 5-phosphate.
{ECO:0000256|HAMAP-Rule:MF_01283}.
BINDING 164 164 D-ribulose 5-phosphate.
{ECO:0000256|HAMAP-Rule:MF_01283}.
BINDING 274 274 GTP. {ECO:0000256|HAMAP-Rule:MF_01283}.
BINDING 318 318 GTP. {ECO:0000256|HAMAP-Rule:MF_01283}.
BINDING 353 353 GTP. {ECO:0000256|HAMAP-Rule:MF_01283}.
BINDING 358 358 GTP. {ECO:0000256|HAMAP-Rule:MF_01283}.
SITE 126 126 Essential for DHBP synthase activity.
{ECO:0000256|HAMAP-Rule:MF_01283}.
SITE 164 164 Essential for DHBP synthase activity.
{ECO:0000256|HAMAP-Rule:MF_01283}.
SEQUENCE 401 AA; 43922 MW; 62F21DD1EFE655CD CRC64;
MPVSRIEDAI EDIRQGKMVI LVDDEDRENE GDLTMAAEKV TPEAINFMAR FGRGLICLSM
TAERCDHLRL PLMVSTNTSS FGTAFTVSIE AKKGVTTGIS AADRAHTILT AVADDCKAED
LARPGHVFPL RAKPGGVLVR AGQTEGSVDL ARLAGLKPAG VICEIMNDDG TMSRLPELRK
FAKEHGIKIC TVADLVAYRL KHESLVRRAA EVKLPTSYGG DFKAIAFEND IDKLEHLALV
KGEIHGDEPV LVRVHSECLT GDVFGSRRCD CCDQLHAAME MIDREGKGVV LYMRQEGRGI
GLINKLKAYA LQDQGQDTVE ANLALGFKAD LRDYGIGAQI LVNLGVKKIR LMTNNPKKIV
GLEGYGINIV ERVSIEVEPT KSNIKYLKTK RDKMGHLIEN I
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Pathways :
WP2340: Thiamine (vitamin B1) biosynthesis and salvage
WP2341: vitamin B1 (thiamin) biosynthesis and salvage pathway
WP1708: Terpenoid backbone biosynthesis
WP2199: Seed Development
WP2208: Cardiolipin Biosynthesis
WP2210: Oryzalexin S biosynthesis
WP2211: Geranylgeranyldiphosphate biosynthesis II (plastidic)
WP2248: anthocyanin biosynthesis
WP626: Abscisic Acid Biosynthesis
WP677: Momilactone biosynthesis
WP1403: AMPK signaling
WP1422: Sphingolipid Metabolism
WP1423: Ganglio Sphingolipid Metabolism
WP1424: Globo Sphingolipid Metabolism
WP1461: Photosynthetic Carbon Reduction
WP1493: Carbon assimilation C4 pathway
WP1621: Arginine and proline metabolism
WP1657: Glycerolipid metabolism
WP1685: Peptidoglycan biosynthesis
WP2339: vitamin B2 (riboflavin) biosynthesis and conversion to FMN and FAD pathway
WP2344: vitamin B6 (pyridoxine, pyridoxal, pyridoxamine) biosynthesis and salvage pathway
WP2349: vitamin B3 (niacin), NAD and NADP biosynthesis pathway
WP2353: vitamin B9 (folate) biosynthesis pathway
WP296: TCA Cycle - biocyc
WP381: Riboflavin, FMN, and FAD Biosynthesis
Related Genes :
Bibliography :
[11024263] Structural and functional analysis of the riboflavin synthesis genes encoding GTP cyclohydrolase II (ribA), DHBP synthase (ribBA), riboflavin synthase (ribC), and riboflavin deaminase/reductase (ribD) from Helicobacter pylori strain P1.
[9515916] Helicobacter pylori ribBA-mediated riboflavin production is involved in iron acquisition.
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