Reviewed, UniProtKB/Swiss-Prot P0A7J0 (RIBB_ECOLI)

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
Synonyms:	htrP
Ordered Locus Names:	b3041, JW3009

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	217 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate. HAMAP MF_00180
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. Ref.6
Pathway	Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1. HAMAP MF_00180
Subunit structure	Homodimer. Ref.6 Ref.7
Subcellular location	Cell membrane; Peripheral membrane protein Potential HAMAP MF_00180.
Induction	Is expressed at all temperatures, but accumulation of transcripts decline with raising temperature. Thus, its expression is repressed by heat shock. HAMAP MF_00180
Sequence similarities	Belongs to the DHBP synthase family.
Mass spectrometry	Molecular mass is 23352±2 Da from positions 1 - 217. Determined by ESI. Ref.3

Ontologies

Keywords
Biological process	Riboflavin biosynthesis Stress response
Cellular component	Cell membrane Membrane
Ligand	Magnesium Manganese Metal-binding
Molecular function	Lyase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	response to stress Inferred from electronic annotation. Source: UniProtKB-KW riboflavin biosynthetic process Inferred from electronic annotation. Source: HAMAP
Cellular component	cytosol Inferred from direct assay. Source: UniProtKB extrinsic to membrane Inferred from electronic annotation. Source: UniProtKB-SubCell plasma membrane Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	3,4-dihydroxy-2-butanone-4-phosphate synthase activity Ref.3 Inferred from direct assay. Source: UniProtKB magnesium ion binding Inferred from electronic annotation. Source: HAMAP manganese ion binding Inferred from electronic annotation. Source: HAMAP protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
cysJ	P38038	1	EBI-553653,EBI-544440

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 217

217

3,4-dihydroxy-2-butanone 4-phosphate synthase HAMAP MF_00180

PRO_0000151797

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 HAMAP MF_00180

Site

174

1

Essential for catalytic activity HAMAP MF_00180

Experimental info

Mutagenesis

33

1

D → S: Loss of activity. Ref.6

Mutagenesis

35

1

E → S: Reduces activity by 85%. Ref.6

Mutagenesis

37

1

R → E: Loss of activity. Ref.6

Mutagenesis

38

1

E → S: Loss of activity. Ref.6

Mutagenesis

40

1

E → S: Loss of activity. Ref.6

Mutagenesis

42

1

D → S: Loss of activity. Ref.6

Mutagenesis

67

1

C → S: Reduces activity by 80%. Ref.6

Mutagenesis

107

1

T → S: Loss of activity. Ref.6

Mutagenesis

110

1

S → A: Reduces activity by 85%. Ref.6

Mutagenesis

113

1

D → S: Reduces activity by 88%. Ref.6

Mutagenesis

117

1

T → A: Reduces activity by 75%. Ref.6

Mutagenesis

136

1

H → S: Loss of activity. Ref.6

Mutagenesis

150

1

R → S: Loss of activity. Ref.6

Mutagenesis

153

1

H → S: Loss of activity. Ref.6

Mutagenesis

155

1

E → S: Reduces activity by 83%. Ref.6

Mutagenesis

174

1

E → S: Loss of activity. Ref.6

Sequence conflict

120 – 123

4

AAIA → SDS in AAA23996. Ref.1

Sequence conflict

211 – 217

7

AHERKAS → HMSVKPAENRCLIYCLNQET EVVAGFGFYFSLLCKMLIPL LFL in AAA23996. Ref.1

Secondary structure

1

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217

Helix Strand Turn

Details...

Helix

6 – 9

4

Helix

12 – 24

13

Beta strand

29 – 33

5

Beta strand

40 – 46

7

Turn

47 – 49

3

Helix

52 – 61

10

Beta strand

67 – 70

4

Helix

72 – 77

6

Beta strand

95 – 97

3

Beta strand

99 – 104

6

Beta strand

106 – 108

3

Helix

111 – 122

12

Helix

128 – 130

3

Beta strand

131 – 141

11

Helix

146 – 148

3

Helix

153 – 163

11

Beta strand

170 – 176

7

Beta strand

180 – 182

3

Helix

185 – 194

10

Beta strand

198 – 201

4

Helix

202 – 212

11

Sequences

	Sequence		Length	Mass (Da)
	P0A7J0-1 [UniParc]. Last modified June 7, 2005. Version 1. Checksum: 6833C120A1442608	FASTA	217	23,353
	10 20 30 40 50 60 MNQTLLSSFG TPFERVENAL AALREGRGVM VLDDEDRENE GDMIFPAETM TVEQMALTIR 70 80 90 100 110 120 HGSGIVCLCI TEDRRKQLDL PMMVENNTSA YGTGFTVTIE AAEGVTTGVS AADRITTVRA 130 140 150 160 170 180 AIADGAKPSD LNRPGHVFPL RAQAGGVLTR GGHTEATIDL MTLAGFKPAG VLCELTNDDG 190 200 210 TMARAPECIE FANKHNMALV TIEDLVAYRQ AHERKAS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The Escherichia coli htrP gene product is essential for bacterial growth at high temperatures: mapping, cloning, sequencing, and transcriptional regulation of htrP." Raina S., Mabey L., Georgopoulos C. J. Bacteriol. 173:5999-6008(1991) [PubMed: 1917833] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Nucleotide sequence of a region duplicated in Escherichia coli toc mutants." Yang T.-P., Depew R.E. Biochim. Biophys. Acta 1130:227-228(1992) [PubMed: 1314093] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Biosynthesis of riboflavin: cloning, sequencing, and expression of the gene coding for 3,4-dihydroxy-2-butanone 4-phosphate synthase of Escherichia coli." Richter G., Volk R., Krieger C., Laham H.-W., Roethlisberger U., Bacher A. J. Bacteriol. 174:4050-4056(1992) [PubMed: 1597419] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE, MASS SPECTROMETRY, CHARACTERIZATION. Strain: K12.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"The NMR structure of the 47-kDa dimeric enzyme 3,4-dihydroxy-2-butanone-4-phosphate synthase and ligand binding studies reveal the location of the active site." Kelly M.J.S., Ball L.J., Krieger C., Yu Y., Fischer M., Schiffmann S., Schmieder P., Kuehne R., Bermel W., Bacher A., Richter G., Oschkinat H. Proc. Natl. Acad. Sci. U.S.A. 98:13025-13030(2001) [PubMed: 11687623] [Abstract] Cited for: STRUCTURE BY NMR, COFACTOR, MUTAGENESIS OF ASP-33; GLU-35; ARG-37; GLU-38; GLU-40; ASP-42; CYS-67; THR-107; SER-110; ASP-113; THR-117; HIS-136; ARG-150; HIS-153; GLU-155 AND GLU-174, SUBUNIT.
[7]	"Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase of riboflavin biosynthesis." Liao D.-I., Calabrese J.C., Wawrzak Z., Viitanen P.V., Jordan D.B. Structure 9:11-18(2001) [PubMed: 11342130] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.40 ANGSTROMS), SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M64472 Genomic DNA. Translation: AAA23996.1.
M77129 Genomic DNA. Translation: AAA71879.1.
X66720 Genomic DNA. Translation: CAA47252.1.
U28377 Genomic DNA. Translation: AAA69209.1.
U00096 Genomic DNA. Translation: AAC76077.1.
AP009048 Genomic DNA. Translation: BAE77097.1.

PIR

A38159.

RefSeq

AP_003591.1.
NP_417513.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1G57	X-ray	1.40	A/B	3-217	[»]
1G58	X-ray	1.55	A/B	3-217	[»]
1IEZ	NMR	-	A	1-217	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P0A7J0. 26 interactions.

STRING

P0A7J0.

Genome annotation databases

GeneID

947526.

GenomeReviews

Gene locus JW3009 in contig AP009048_GR.
Gene locus b3041 in contig U00096_GR.

KEGG

ecj:JW3009.
eco:b3041.

Organism-specific databases

EchoBASE

EB0460.

EcoGene

EG10465. ribB.

CMR

Search...

Phylogenomic databases

eggNOG

COG0108.

HOGENOM

HBG735778.

OMA

RGHTEAT.

Enzyme and pathway databases

BioCyc

EcoCyc:DIOHBUTANONEPSYN-MONOMER.
ECOL168927:B3041-MONOMER.
MetaCyc:DIOHBUTANONEPSYN-MONOMER.

BRENDA

4.1.99.12. 190306.

Gene expression databases

Genevestigator

P0A7J0.

Family and domain databases

HAMAP

MF_00180. RibB.
[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]

TIGRFAMs

TIGR00506. ribB. 1 hit.

ProtoNet

Search...

Entry information

Entry name

RIBB_ECOLI

Accession

Primary (citable) accession number: P0A7J0
Secondary accession number(s): P24199, Q2M9F9

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 7, 2005
Last sequence update:	June 7, 2005
Last modified:	February 9, 2010
This is version 50 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)