Reviewed, UniProtKB/Swiss-Prot Q60364 (RIBB_METJA)

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:	MJ0055

Organism

Methanocaldococcus jannaschii (Methanococcus jannaschii) [Complete proteome] [HAMAP]

Taxonomic identifier

2190 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanococci › Methanococcales › Methanocaldococcaceae › Methanocaldococcus

Protein attributes

Sequence length	227 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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.
Catalytic activity	D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate.
Cofactor	Binds 2 divalent metal cations per subunit. Magnesium or manganese.
Pathway	Cofactor biosynthesis; riboflavin biosynthesis; 3,4-dihydroxy-2-butanone 4-phosphate from D-ribulose 5-phosphate: step 1/1.
Subunit structure	Homodimer.
Sequence similarities	Belongs to the DHBP synthase family.
Biophysicochemical properties	Kinetic parameters: KM=140 µM for ribulose-5-phosphate Vmax=148 nmol/min/mg enzyme
Mass spectrometry	Molecular weight is 25799 Da from positions 1 - 227. Determined by ESI. Ref.2

Ontologies

Keywords
Biological process	Riboflavin biosynthesis
Ligand	Magnesium Manganese Metal-binding
Molecular function	Lyase
Technical term	3D-structure Complete proteome Direct protein sequencing
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

Molecule processing

Chain

1 – 227

227

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

Regions

Region

25 – 26

2

Substrate binding

Region

161 – 165

5

Substrate binding

Sites

Metal binding

26

1

Magnesium or manganese 1

Metal binding

26

1

Magnesium or manganese 2

Metal binding

164

1

Magnesium or manganese 2

Binding site

30

1

Substrate

Binding site

185

1

Substrate

Site

147

1

Essential for catalytic activity

Site

185

1

Essential for catalytic activity

Experimental info

Mutagenesis

21

1

D → E or N: Loss of activity

Mutagenesis

21

1

D → S: Reduces activity 70-fold

Mutagenesis

25

1

R → E or K: Reduces activity 50-fold

Mutagenesis

26

1

E → D, Q or S: Loss of activity

Mutagenesis

28

1

E → D or S: Loss of activity

Mutagenesis

28

1

E → Q: Reduces activity 23-fold

Mutagenesis

30

1

D → E or N: Loss of activity

Mutagenesis

30

1

D → S: Reduces activity 30-fold

Mutagenesis

55

1

C → G: Reduces activity 70-fold. Increases Km for ribulose-5-phosphate 7-fold

Mutagenesis

55

1

C → S: Reduces activity 30-fold

Mutagenesis

112

1

T → A: Reduces activity 50-fold. Increases Km for ribulose-5-phosphate 10-fold

Mutagenesis

119

1

R → S: Reduces activity 8-fold. Increases Km for ribulose-5-phosphate 8-fold

Mutagenesis

147

1

H → S: Reduces activity 10-fold

Mutagenesis

161

1

R → S: Reduces activity 10-fold. Increases Km for ribulose-5-phosphate 7-fold

Mutagenesis

164

1

H → N or S: Loss of activity

Mutagenesis

165

1

T → A: Reduces activity by 2-fold. Increases Km for ribulose-5-phosphate 8-fold

Mutagenesis

165

1

T → S: Reduces activity by 3-fold

Mutagenesis

166

1

E → S: Increases Km for ribulose-5-phosphate 8-fold

Mutagenesis

185

1

E → D, Q or S: Loss of activity

Secondary structure

1

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227

Helix Strand Turn

Details...

Helix

3 – 12

10

Beta strand

17 – 20

4

Turn

23 – 26

4

Beta strand

29 – 34

6

Helix

35 – 37

3

Helix

40 – 49

10

Beta strand

55 – 58

4

Helix

60 – 66

7

Helix

71 – 78

8

Turn

79 – 81

3

Helix

84 – 87

4

Beta strand

94 – 98

5

Beta strand

101 – 107

7

Beta strand

111 – 113

3

Helix

116 – 131

16

Helix

135 – 137

3

Helix

138 – 141

4

Beta strand

142 – 152

11

Helix

157 – 159

3

Helix

164 – 174

11

Beta strand

179 – 187

9

Beta strand

191 – 193

3

Helix

196 – 204

9

Turn

205 – 207

3

Beta strand

209 – 212

4

Helix

213 – 219

7

Sequences

	Sequence		Length	Mass (Da)
	Q60364-1 [UniParc]. Last modified November 1, 1997. Version 1. Checksum: 0718EE5B4247995D	FASTA	227	25,797
	10 20 30 40 50 60 MNNVEKAIEA LKKGEIILVY DSDEREGETD MVVASQFITP EHIRIMRKDA GGLICTALHP 70 80 90 100 110 120 DICNKLGIPF MVDILEFASQ KFKVLRELYP NDIPYDEKSS FSITINHRKT FTGITDNDRA 130 140 150 160 170 180 FTIKKLAELV KEGRFNDFGK EFRSPGHVTL LRAAEGLVKN RQGHTEMTVA LAELANLVPI 190 200 210 220 TTICEMMGDD GNAMSKNETK RYAEKHNLIY LSGEEIINYY LDKYLKD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii." Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G., Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R., Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R., Kirkness E.F., Weinstock K.G. , Merrick J.M., Glodek A., Scott J.L., Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R., Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D., Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P., Fraser C.M., Smith H.O., Woese C.R., Venter J.C. Science 273:1058-1073(1996) [PubMed: 8688087] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
[2]	"Biosynthesis of riboflavin in archaea studies on the mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase of Methanococcus jannaschii." Fischer M., Roemisch W., Schiffmann S., Kelly M., Oschkinat H., Steinbacher S., Huber R., Eisenreich W., Richter G., Bacher A. J. Biol. Chem. 277:41410-41416(2002) [PubMed: 12200440] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-15, FUNCTION, MASS SPECTROMETRY, BIOPHYSOCOCHEMICAL PROPERTIES, SUBUNIT, COFACTOR, MUTAGENESIS OF ASP-21; ARG-25; GLU-26; GLU-28; ASP-30; CYS-55; THR-112; ARG-119; ARG-161; HIS-164; THR-165; GLU-166 AND GLU-185.
[3]	"Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism." Steinbacher S., Schiffmann S., Richter G., Huber R., Bacher A., Fischer M. J. Biol. Chem. 278:42256-42265(2003) [PubMed: 12904291] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF MUTANT SER-147 IN COMPLEX WITH DIVALENT METAL CATIONS AND SUBSTRATE, SUBUNIT.
[4]	"Metal sites in 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with the substrate ribulose 5-phosphate." Steinbacher S., Schiffmann S., Bacher A., Fischer M. Acta Crystallogr. D 60:1338-1340(2004) [PubMed: 15213409] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF MUTANT SER-147 IN COMPLEX WITH DIVALENT METAL CATIONS AND SUBSTRATE, SUBUNIT.

Cross-references

Sequence databases

EMBLGenBankDDBJ

L77117 Genomic DNA. Translation: AAB98035.1.

PIR

G64306.

RefSeq

NP_247019.1.

3D structure databases

PDBMSD

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1PVW	X-ray	2.45	A/B/C	1-227	[»]
1PVY	X-ray	1.70	A/B	1-227	[»]
1SNN	X-ray	1.55	A/B	1-227	[»]

ModBase

Search...

Genome annotation databases

GeneID

1450894.

GenomeReviews

Gene locus MJ0055 in contig L77117_GR.

KEGG

mja:MJ0055.

NMPDR

fig|243232.1.peg.56.

TIGR

MJ0055.

Phylogenomic databases

HOGENOM

Q60364.

Enzyme and pathway databases

BioCyc

MJAN243232:MJ_0055-MON.

Family and domain databases

HAMAP

MF_00180.
[Tree]

InterPro

IPR000422. DHBP_synthase.
[Graphical view]

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.

BLOCKS

Search...

Other Resources

ProtoNet

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Entry information

Entry name

RIBB_METJA

Accession

Primary (citable) accession number: Q60364

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	July 22, 2008
This is version 54 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)