Reviewed, UniProtKB/Swiss-Prot A1VD83 (RIBB_DESVV)

Names and origin

Protein names

Recommended name:
    3,4-dihydroxy-2-butanone 4-phosphate synthase
      Short name=DHBP synthase
    EC=4.1.99.12

Gene names

Name:	ribB
Ordered Locus Names:	Dvul_1381

Organism

Desulfovibrio vulgaris subsp. vulgaris (strain DP4) [Complete proteome] [HAMAP]

Taxonomic identifier

391774 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio

Protein attributes

Sequence length	214 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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.
Catalytic activity	D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate. HAMAP MF_00180
Cofactor	Binds 2 divalent metal cations per subunit. Magnesium or manganese By similarity.
Pathway	Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1. HAMAP MF_00180
Subunit structure	Homodimer By similarity.
Sequence similarities	Belongs to the DHBP synthase family.

Ontologies

Keywords
Biological process	Riboflavin biosynthesis
Ligand	Magnesium Manganese Metal-binding
Molecular function	Lyase
Technical term	Complete proteome
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 magnesium ion binding Inferred from electronic annotation. Source: HAMAP manganese 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 – 214	214	3,4-dihydroxy-2-butanone 4-phosphate synthase HAMAP MF_00180		PRO_1000040604
Regions
	Region	37 – 38	2	Substrate binding By similarity
	Region	150 – 154	5	Substrate binding By similarity
Sites
	Metal binding	38	1	Magnesium or manganese 1 By similarity
	Metal binding	38	1	Magnesium or manganese 2 By similarity
	Metal binding	153	1	Magnesium or manganese 2 By similarity
	Binding site	42	1	Substrate By similarity
	Binding site	174	1	Substrate By similarity
	Site	136	1	Essential for catalytic activity By similarity
	Site	174	1	Essential for catalytic activity By similarity

Sequences

	Sequence		Length	Mass (Da)
	A1VD83-1 [UniParc]. Last modified February 6, 2007. Version 1. Checksum: 967CE6551A09FAF2	FASTA	214	23,033
	10 20 30 40 50 60 MNQHLLEQFG TTHERVERGL AALRTGQGVL VADDADRENE GDLIFAAETL TPAQMAMMIR 70 80 90 100 110 120 ECSGIVCLCL PEERVSRLGL PMMVAHNTSS MGTAFTISIE AAEGVTTGVS AADRVRTVQA 130 140 150 160 170 180 AIDDAACPGC LRSPGHVFPL RASPGGVLER RGHTEATVDL MRLAGLKPYG VLCELTNPDG 190 200 210 TMARLPQLVD FAQRNRMTVL TVEDLVAYRQ DKGL

References

[1]

"Complete sequence of chromosome 1 of Desulfovibrio vulgaris subsp. vulgaris DP4." Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N. , Lykidis A., Walker C., Richardson P. Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	CP000527 Genomic DNA. Translation: ABM28399.1.
RefSeq	YP_966826.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	A1VD83.
Genome annotation databases
GeneID	4664833.
GenomeReviews	Gene locus Dvul_1381 in contig CP000527_GR.
KEGG	dvl:Dvul_1381.
NMPDR	fig|391774.5.peg.1409.
Organism-specific databases
CMR	Search...
Phylogenomic databases
OMA	YGSGIVC.
Family and domain databases
HAMAP	MF_00180. [Tree]
InterPro	IPR017945. DHBP_synth_RibB-like_a/b_dom. IPR000422. DHBP_synthase_RibB. [Graphical view]
Gene3D	G3DSA:3.90.870.10. DHBP_synth_RibB-like_a/b_dom. 1 hit.
Pfam	PF00926. DHBP_synthase. 1 hit. [Graphical view]
ProDom	PD003034. DHBP_synthase. 1 hit. [Graphical view] [Entries sharing at least one domain]
TIGRFAMs	TIGR00506. ribB. 1 hit.
ProtoNet	Search...

Entry information

Entry name

RIBB_DESVV

Accession

Primary (citable) accession number: A1VD83

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	February 6, 2007
Last modified:	November 3, 2009
This is version 20 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)