HAMAP rule MF_01283
General rule information
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| Accession | MF_01283 |
| Dates | 16-NOV-2007 (Created)
3-SEP-2024 (Last updated, Version 21) |
| Name | RibBA |
| Scope(s) |
Bacteria |
| Template(s) | P50855 (RIBBA_ACTPL); [ Recover all ] |
| Triggered by |
HAMAP; MF_01283 (Get profile general information and statistics) |
Propagated annotation
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Identifier, protein and gene names
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| Identifier | RIBBA |
| Protein name | RecName: Full=Riboflavin biosynthesis protein RibBA; Includes: RecName: Full=3,4-dihydroxy-2-butanone 4-phosphate synthase; Short=DHBP synthase; EC=4.1.99.12; Includes: RecName: Full=GTP cyclohydrolase-2; EC=3.5.4.25; AltName: Full=GTP cyclohydrolase II; |
| Gene name | Name=ribBA; |
Comments
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| FUNCTION | Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate. |
| FUNCTION | Catalyzes the conversion of GTP to 2,5-diamino-6- ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and pyrophosphate. |
| 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; |
| CATALYTIC ACTIVITY | Reaction=GTP + 4 H2O = 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)- pyrimidine + formate + 2 phosphate + 3 H(+); Xref=Rhea:RHEA:23704, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:15740, ChEBI:CHEBI:37565, ChEBI:CHEBI:43474, ChEBI:CHEBI:58614; EC=3.5.4.25; |
| COFACTOR | Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Note=Binds 2 divalent metal cations per subunit. Magnesium or manganese.; |
| COFACTOR | Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Note=Binds 1 zinc ion per subunit.; |
| PATHWAY | Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3- oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1. |
| PATHWAY | Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D- ribitylamino)uracil from GTP: step 1/4. |
| SIMILARITY | In the N-terminal section; belongs to the DHBP synthase family. |
| SIMILARITY | In the C-terminal section; belongs to the GTP cyclohydrolase II family. |
Keywords
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| GTP-binding |
| Hydrolase |
| Lyase |
| Magnesium |
| Manganese |
| Metal-binding |
| Multifunctional enzyme |
| Nucleotide-binding |
| Riboflavin biosynthesis |
| Zinc |
Gene Ontology
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| GO:0000287; Molecular function:magnesium ion binding |
| GO:0003935; Molecular function:GTP cyclohydrolase II activity |
| GO:0008270; Molecular function:zinc ion binding |
| GO:0008686; Molecular function:3,4-dihydroxy-2-butanone-4-phosphate synthase activity |
| GO:0030145; Molecular function:manganese ion binding |
| GO:0009231; Biological process:riboflavin biosynthetic process |
Cross-references
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| Pfam | PF00926; DHBP_synthase; 1; |
| Pfam | PF00925; GTP_cyclohydro2; 1; |
| NCBIfam | TIGR00505; RibA; 1; |
| NCBIfam | TIGR00506; RibB; 1; |
Features
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| From: RIBBA_BACSU (P17620) | ||||||||||||
| Key | From | To | Description | Tag | Condition | FTGroup | ||||||
| BINDING | 251 | 255 | /ligand="GTP" /ligand_id="ChEBI:CHEBI:37565" |
|||||||||
| BINDING | 294 | 296 | /ligand="GTP" /ligand_id="ChEBI:CHEBI:37565" |
E-G-R | ||||||||
| REGION | Nter | 199 | /note="DHBP synthase" | |||||||||
| BINDING | 26 | 27 | /ligand="D-ribulose 5-phosphate" /ligand_id="ChEBI:CHEBI:58121" |
R-E | ||||||||
| BINDING | 138 | 142 | /ligand="D-ribulose 5-phosphate" /ligand_id="ChEBI:CHEBI:58121" |
R-x-x-H-T | ||||||||
| REGION | 200 | Cter | /note="GTP cyclohydrolase II" | |||||||||
| ACT_SITE | 328 | 328 | /note="Proton acceptor; for GTP cyclohydrolase activity" | D | ||||||||
| ACT_SITE | 330 | 330 | /note="Nucleophile; for GTP cyclohydrolase activity" | R | ||||||||
| BINDING | 27 | 27 | /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="1" |
E | ||||||||
| BINDING | 27 | 27 | /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="2" |
E | ||||||||
| BINDING | 141 | 141 | /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="2" |
H | ||||||||
| BINDING | 256 | 256 | /ligand="Zn(2+)" /ligand_id="ChEBI:CHEBI:29105" /ligand_note="catalytic" |
C | ||||||||
| BINDING | 267 | 267 | /ligand="Zn(2+)" /ligand_id="ChEBI:CHEBI:29105" /ligand_note="catalytic" |
C | ||||||||
| BINDING | 269 | 269 | /ligand="Zn(2+)" /ligand_id="ChEBI:CHEBI:29105" /ligand_note="catalytic" |
C | ||||||||
| BINDING | 31 | 31 | /ligand="D-ribulose 5-phosphate" /ligand_id="ChEBI:CHEBI:58121" |
D | ||||||||
| BINDING | 162 | 162 | /ligand="D-ribulose 5-phosphate" /ligand_id="ChEBI:CHEBI:58121" |
E | ||||||||
| BINDING | 272 | 272 | /ligand="GTP" /ligand_id="ChEBI:CHEBI:37565" |
Q | ||||||||
| BINDING | 316 | 316 | /ligand="GTP" /ligand_id="ChEBI:CHEBI:37565" |
T | ||||||||
| BINDING | 351 | 351 | /ligand="GTP" /ligand_id="ChEBI:CHEBI:37565" |
[TS] | ||||||||
| BINDING | 356 | 356 | /ligand="GTP" /ligand_id="ChEBI:CHEBI:37565" |
K | ||||||||
| SITE | 124 | 124 | /note="Essential for DHBP synthase activity" | H | ||||||||
| SITE | 162 | 162 | /note="Essential for DHBP synthase activity" | E | ||||||||
Additional information
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| Size range | 388-425 amino acids |
| Related rules |
MF_00178 MF_00179 |
| Fusion | Nter: None Cter: <Unknown> |
| Comments | RibA and RibB are not fused in some organisms (see MF_00179 for RibA and MF_00180 for RibB). Fused with an unknown C-terminal domain in SYNY3. |