Reviewed, UniProtKB/Swiss-Prot Q5HNE3 (RIBBA_STAEQ)

Names and origin

Protein names

Recommended name:
    Riboflavin biosynthesis protein ribBA
Including the following 2 domains:
    1- Recommended name:
            3,4-dihydroxy-2-butanone 4-phosphate synthase
                Short name=DHBP synthase
              EC=4.1.99.12
    2- Recommended name:
            GTP cyclohydrolase-2
              EC=3.5.4.25
        Alternative name(s):
            GTP cyclohydrolase II

Gene names

Name:	ribBA
Ordered Locus Names:	SERP1326

Organism

Staphylococcus epidermidis (strain ATCC 35984 / RP62A) [Complete proteome] [HAMAP]

Taxonomic identifier

176279 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Staphylococcus

Protein attributes

Sequence length	393 AA.
Sequence status	Complete.
Protein existence	Inferred from homology.

General annotation (Comments)

Function	Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate By similarity. HAMAP MF_01283 Catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and pyrophosphate By similarity. HAMAP MF_01283
Catalytic activity	D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate. HAMAP MF_01283 GTP + 3 H2O = formate + 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + diphosphate. HAMAP MF_01283
Cofactor	Binds 2 divalent metal cations per subunit. Magnesium or manganese By similarity. HAMAP MF_01283 Binds 1 zinc ion per subunit By similarity. HAMAP MF_01283
Pathway	Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1. HAMAP MF_01283 Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-ribitylamino)uracil from GTP: step 1/4. HAMAP MF_01283
Sequence similarities	In the N-terminal section; belongs to the DHBP synthase family. In the C-terminal section; belongs to the GTP cyclohydrolase II family.

Ontologies

Keywords
Biological process	Riboflavin biosynthesis
Ligand	GTP-binding Magnesium Manganese Metal-binding Nucleotide-binding Zinc
Molecular function	Hydrolase Lyase
Technical term	Complete proteome Multifunctional enzyme
Gene Ontology (GO)
Biological process	riboflavin biosynthetic process Inferred from electronic annotation. Source: HAMAP
Molecular function	3,4-dihydroxy-2-butanone-4-phosphate synthase activity Inferred from electronic annotation. Source: HAMAP GTP binding Inferred from electronic annotation. Source: UniProtKB-KW GTP cyclohydrolase II activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: HAMAP manganese ion binding Inferred from electronic annotation. Source: HAMAP zinc ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 393	393	Riboflavin biosynthesis protein ribBA HAMAP MF_01283		PRO_0000151740
Regions
	Nucleotide binding	249 – 253	5	GTP By similarity
	Nucleotide binding	291 – 293	3	GTP By similarity
	Region	1 – 200	200	DHBP synthase HAMAP MF_01283
	Region	27 – 28	2	D-ribulose 5-phosphate binding By similarity
	Region	139 – 143	5	D-ribulose 5-phosphate binding By similarity
	Region	201 – 393	193	GTP cyclohydrolase II HAMAP MF_01283
Sites
	Active site	325	1	Proton acceptor; for GTP cyclohydrolase activity Potential
	Active site	327	1	Nucleophile; for GTP cyclohydrolase activity By similarity
	Metal binding	28	1	Magnesium or manganese 1 By similarity
	Metal binding	28	1	Magnesium or manganese 2 By similarity
	Metal binding	142	1	Magnesium or manganese 2 By similarity
	Metal binding	254	1	Zinc; catalytic By similarity
	Metal binding	265	1	Zinc; catalytic By similarity
	Metal binding	267	1	Zinc; catalytic By similarity
	Binding site	32	1	D-ribulose 5-phosphate By similarity
	Binding site	163	1	D-ribulose 5-phosphate By similarity
	Binding site	270	1	GTP By similarity
	Binding site	313	1	GTP By similarity
	Binding site	348	1	GTP By similarity
	Binding site	353	1	GTP By similarity
	Site	125	1	Essential for DHBP synthase activity By similarity
	Site	163	1	Essential for DHBP synthase activity By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q5HNE3-1 [UniParc]. Last modified February 15, 2005. Version 1. Checksum: C12B8589078DF592	FASTA	393	44,290
	10 20 30 40 50 60 MQFDTIELAI EALRNGESII VVDDEDRENE GDLVAVTEWM DDNTINFMAR EGRGLICAPI 70 80 90 100 110 120 DKSIAERLKL QSMEQNNTDI YGTHFTVSID HYKTTTGISA HERTQTARAL IDENTNPEDF 130 140 150 160 170 180 HRPGHLFPLI AKENGVLTRN GHTEAAVDLA RLTGAQPAGV ICEIMNDDGT MAKGEDLQSF 190 200 210 220 230 240 KERHHLKMIT IKSLVAFRKA VELNVNLKAK VKMPTDFGHF DMYGFTTNYS DEEIVAIVKG 250 260 270 280 290 300 DLKSNPNVRM HSACLTGDIF HSQRCDCGAQ LEASMKYIDE HGGMIIYLPQ EGRGIGLINK 310 320 330 340 350 360 LRAYELIEKG YDTVTANLAL GFDEDLRDYH VAAEILKYFD ISEINLLSNN PKKFEGLEDY 370 380 390 GIEIVDRIEL IVPETQYNHS YMETKKNKMG HLI

References

[1]

"Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain." Gill S.R., Fouts D.E., Archer G.L., Mongodin E.F., DeBoy R.T., Ravel J., Paulsen I.T., Kolonay J.F., Brinkac L.M., Beanan M.J., Dodson R.J., Daugherty S.C., Madupu R., Angiuoli S.V., Durkin A.S., Haft D.H., Vamathevan J.J., Khouri H. , Utterback T.R., Lee C., Dimitrov G., Jiang L., Qin H., Weidman J., Tran K., Kang K.H., Hance I.R., Nelson K.E., Fraser C.M. J. Bacteriol. 187:2426-2438(2005) [PubMed: 15774886] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000029 Genomic DNA. Translation: AAW54662.1.
RefSeq	YP_188898.1.
3D structure databases
SMR	Q5HNE3. Positions 2-202, 206-372.
ModBase	Search...
Protein-protein interaction databases
STRING	Q5HNE3.
Genome annotation databases
GeneID	3241713.
GenomeReviews	Gene locus SERP1326 in contig CP000029_GR.
KEGG	ser:SERP1326.
NMPDR	fig|176279.3.peg.1153.
TIGR	SERP1326.
Phylogenomic databases
eggNOG	COG0108.
HOGENOM	HBG735778.
OMA	LRCDCRM.
Enzyme and pathway databases
BioCyc	SEPI176279:SERP1326-MONOMER.
Family and domain databases
HAMAP	MF_01283. RibBA. [Tree]
InterPro	IPR017945. DHBP_synth_RibB-like_a/b_dom. IPR000422. DHBP_synthase_RibB. IPR000926. GTP_CycHdrlase_II. IPR016299. Riboflavin_synth_RibA. [Graphical view]
Gene3D	G3DSA:3.90.870.10. DHBP_synth_RibB-like_a/b_dom. 1 hit.
Pfam	PF00926. DHBP_synthase. 1 hit. PF00925. GTP_cyclohydro2. 1 hit. [Graphical view]
PIRSF	PIRSF001259. RibA. 1 hit.
TIGRFAMs	TIGR00505. ribA. 1 hit. TIGR00506. ribB. 1 hit.
ProtoNet	Search...

Entry information

Entry name

RIBBA_STAEQ

Accession

Primary (citable) accession number: Q5HNE3

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 22, 2005
Last sequence update:	February 15, 2005
Last modified:	February 9, 2010
This is version 42 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)