ribA

ribA
168

GTP cyclohydrolase II/ 3,4-dihydroxy-2-butanone 4-phosphate synthase

Locus
BSU_23260
Molecular weight
43.96 kDa
Isoelectric point
5.58
Protein length
398 aaSequenceBlast
Gene length
1197 bpSequenceBlast
Function
riboflavin biosynthesis
Product
GTP cyclohydrolase II/ 3,4-dihydroxy-2-butanone 4-phosphate synthase
Essential
no
E.C.
3.5.4.25
Synonyms
ribA, ribBA
Outlinks
BsubCyc SubtiList UniProt STRING Genoscapist PaperBLAST

Genomic Context

Categories containing this gene/protein

List of homologs in different organisms, belongs to COG0807 (Galperin et al., 2021)

This gene is a member of the following regulons

Gene
Coordinates
2,428,389 → 2,429,585
The protein
Catalyzed reaction/ biological activity
D-ribulose 5-phosphate --> (2S)-2-hydroxy-3-oxobutyl phosphate + formate + H+ (according to UniProt)
GTP + 3 H2O --> 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + diphosphate + formate + 2 H+ (according to UniProt)
Protein family
N-terminal part: DHBP synthase family (single member, according to UniProt)
C-terminal part: GTP cyclohydrolase II family (single member, according to UniProt)
Structure
2BZ0 (PDB) (from E. coli, 54% identity, 69% similarity to  the C-terminal domain) PubMed
P17620 (AlphaFold)
Localization
cytoplasm PubMed
Expression and Regulation
Operons
Genes
ribD-ribE-ribA-ribH-ribT
Description
PubMed
Regulation
expressed in the absence of FMN (FMN-box) PubMed
binding of RibR to the FMN-box riboswitch can enforce expression even in the presence of FMN PubMed
the FMN-box RNA is degraded by RNase Y PubMed
Regulatory mechanism
FMN-box: RNA switch, via FMN-box in the presence of FMN or FMNH2, this is counter-acted upon binding of RibR, in FMN-box
RibR: antitermination, PubMed, in ribR regulon
Sigma factors
SigA: sigma factor, PubMed, in sigA regulon
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ribD→ribT

2025-04-16 00:23:22

Jstuelk

124

3D660447137821317811200D29A5FC04A41E938E

05C8A4E892E7DB3D953FE72E8765638644759326

Biological materials
Mutant
BKE23260 (ΔribA::erm  trpC2) available at BGSC,  PubMed, upstream reverse: _UP1_ATGAAACATGCAAATCTTCC,  downstream forward: _UP4_TAATCACAAATATCACAAAA
BKK23260 (ΔribA::kan  trpC2) available at BGSC,  PubMed, upstream reverse: _UP1_ATGAAACATGCAAATCTTCC,  downstream forward: _UP4_TAATCACAAATATCACAAAA
References
Rotter DAO, Heger C, Oviedo-Bocanegra LM, Graumann PLTranscription-dependent confined diffusion of enzymes within subcellular spaces of the bacterial cytoplasm.BMC biology. 2021 Sep 2; 19(1):183. PMID: 34474681
Pedrolli DB, Kühm C, Sévin DC, Vockenhuber MP, Sauer U, Suess B, Mack M A dual control mechanism synchronizes riboflavin and sulphur metabolism in Bacillus subtilis. Proceedings of the National Academy of Sciences of the United States of America. 2015 Nov 10; 112(45):14054-9. doi:10.1073/pnas.1515024112. PMID:26494285
Birkenmeier M, Mack M, Röder T Thermodynamic and Probabilistic Metabolic Control Analysis of Riboflavin (Vitamin B₂) Biosynthesis in Bacteria. Applied biochemistry and biotechnology. 2015 Oct; 177(3):732-52. doi:10.1007/s12010-015-1776-y. PMID:26280801
Birkenmeier M, Neumann S, Röder T Kinetic modeling of riboflavin biosynthesis in Bacillus subtilis under production conditions. Biotechnology letters. 2014 May; 36(5):919-28. doi:10.1007/s10529-013-1435-8. PMID:24442413
Skliarova SA, Kreneva RA, Perumov DA, Mironov AS [The characterization of internal promoters in the Bacillus subtilis riboflavin biosynthesis operon]. Genetika. 2012 Oct; 48(10):1133-41. . PMID:23270261
Lehmann M, Degen S, Hohmann HP, Wyss M, Bacher A, Schramek N Biosynthesis of riboflavin. Screening for an improved GTP cyclohydrolase II mutant. The FEBS journal. 2009 Aug; 276(15):4119-29. doi:10.1111/j.1742-4658.2009.07118.x. PMID:19583770
Ren J, Kotaka M, Lockyer M, Lamb HK, Hawkins AR, Stammers DK GTP cyclohydrolase II structure and mechanism. The Journal of biological chemistry. 2005 Nov 04; 280(44):36912-9. . PMID:16115872
Wickiser JK, Winkler WC, Breaker RR, Crothers DM The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Molecular cell. 2005 Apr 01; 18(1):49-60. . PMID:15808508
Winkler WC, Cohen-Chalamish S, Breaker RR An mRNA structure that controls gene expression by binding FMN. Proceedings of the National Academy of Sciences of the United States of America. 2002 Dec 10; 99(25):15908-13. . PMID:12456892
Mironov VN, Kraev AS, Chikindas ML, Chernov BK, Stepanov AI, Skryabin KG Functional organization of the riboflavin biosynthesis operon from Bacillus subtilis SHgw. Molecular & general genetics : MGG. 1994 Jan; 242(2):201-8. . PMID:8159171
Azevedo V, Sorokin A, Ehrlich SD, Serror P The transcriptional organization of the Bacillus subtilis 168 chromosome region between the spoVAF and serA genetic loci. Molecular microbiology. 1993 Oct; 10(2):397-405. . PMID:7934830
Sorokin A, Zumstein E, Azevedo V, Ehrlich SD, Serror P The organization of the Bacillus subtilis 168 chromosome region between the spoVA and serA genetic loci, based on sequence data. Molecular microbiology. 1993 Oct; 10(2):385-95. . PMID:7934829

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Time of last update: 2025-04-16 10:52:18

Author of last update: Jstuelk