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HAMAP rule MF_01283

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General rule information [?]

Accession MF_01283
Dates 16-NOV-2007 (Created)
19-NOV-2022 (Last updated, Version 19)
Name RibBA
Scope
Bacteria
Template P50855 (RIBBA_ACTPL)
Triggered by

Propagated annotation [?]


Identifier, protein and gene names [?]

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
ribBA

Comments [?]

Function Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.
Catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and pyrophosphate.
Catalytic activity RHEA:18457: D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate + formate + H(+)
EC 4.1.99.12
RHEA:23704: GTP + 4 H2O = 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + formate + 3 H(+) + 2 phosphate
EC 3.5.4.25
Cofactor Mg(2+)
Mn(2+)
Note: Binds 2 divalent metal cations per subunit. Magnesium or manganese.
Zn(2+)
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.
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.
In the C-terminal section; belongs to the GTP cyclohydrolase II family.

Keywords [?]

GTP-binding
Hydrolase
Lyase
Magnesium
Manganese
Metal-binding
Multifunctional enzyme
Nucleotide-binding
Riboflavin biosynthesis
Zinc

Gene Ontology [?]

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 [?]

Pfam PF00926; DHBP_synthase; 1;
PF00925; GTP_cyclohydro2; 1;
TIGRFAMs TIGR00505; RibA; 1;
TIGR00506; RibB; 1;

Features [?]

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       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       GTP cyclohydrolase II        
ACT_SITE     328     328       Proton acceptor; for GTP cyclohydrolase activity     D  
ACT_SITE     330     330       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       Essential for DHBP synthase activity     H  
SITE     162     162       Essential for DHBP synthase activity     E  

Additional information [?]

Size range 388-425 amino acids
Related rules MF_00178 (RISB); MF_00179 (RIBA)
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.


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