Q60364 (RIBB_METJA) Reviewed, UniProtKB/Swiss-Prot

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 (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) [Reference proteome] [HAMAP]

Taxonomic identifier

243232 [NCBI]

Taxonomic lineage

cellular organisms › Archaea › Euryarchaeota › Methanococci › Methanococcales › Methanocaldococcaceae › Methanocaldococcus › Methanocaldococcus jannaschii

Protein attributes

Sequence length	227 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. Ref.2
Catalytic activity	D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate. HAMAP-Rule MF_00180
Cofactor	Binds 2 divalent metal cations per subunit. Magnesium or manganese. Ref.2
Pathway	Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1. HAMAP-Rule MF_00180
Subunit structure	Homodimer. Ref.2 Ref.3 Ref.4
Sequence similarities	Belongs to the DHBP synthase family.
Biophysicochemical properties	Kinetic parameters: KM=140 µM for ribulose-5-phosphate Ref.2 Vmax=148 nmol/min/mg enzyme
Mass spectrometry	Molecular mass 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 Reference 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 – 227

227

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

PRO_0000151825

Regions

Region

25 – 26

2

Substrate binding HAMAP-Rule MF_00180

Region

161 – 165

5

Substrate binding HAMAP-Rule MF_00180

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. Ref.2

Mutagenesis

21

1

D → S: Reduces activity 70-fold. Ref.2

Mutagenesis

25

1

R → E or K: Reduces activity 50-fold. Ref.2

Mutagenesis

26

1

E → D, Q or S: Loss of activity. Ref.2

Mutagenesis

28

1

E → D or S: Loss of activity. Ref.2

Mutagenesis

28

1

E → Q: Reduces activity 23-fold. Ref.2

Mutagenesis

30

1

D → E or N: Loss of activity. Ref.2

Mutagenesis

30

1

D → S: Reduces activity 30-fold. Ref.2

Mutagenesis

55

1

C → G: Reduces activity 70-fold. Increases Km for ribulose-5-phosphate 7-fold. Ref.2

Mutagenesis

55

1

C → S: Reduces activity 30-fold. Ref.2

Mutagenesis

112

1

T → A: Reduces activity 50-fold. Increases Km for ribulose-5-phosphate 10-fold. Ref.2

Mutagenesis

119

1

R → S: Reduces activity 8-fold. Increases Km for ribulose-5-phosphate 8-fold. Ref.2

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. Ref.2

Mutagenesis

164

1

H → N or S: Loss of activity. Ref.2

Mutagenesis

165

1

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

Mutagenesis

165

1

T → S: Reduces activity by 3-fold. Ref.2

Mutagenesis

166

1

E → S: Increases Km for ribulose-5-phosphate 8-fold. Ref.2

Mutagenesis

185

1

E → D, Q or S: Loss of activity. Ref.2

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

51 – 58

8

Helix

60 – 66

7

Helix

71 – 78

8

Turn

79 – 81

3

Helix

83 – 87

5

Beta strand

96 – 98

3

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 – 206

11

Beta strand

210 – 212

3

Helix

213 – 219

7

Sequences

	Sequence		Length	Mass (Da)
	Q60364 [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-15, FUNCTION, MASS SPECTROMETRY, BIOPHYSICOCHEMICAL 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] [Europe PMC] [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] [Europe PMC] [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

EMBL
GenBank
DDBJ

L77117 Genomic DNA. Translation: AAB98035.1.

PIR

G64306.

RefSeq

NP_247019.1. NC_000909.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

Q60364.

SMR

Q60364. Positions 2-220.

ModBase

Search...

Protein-protein interaction databases

STRING

243232.MJ0055.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAB98035; AAB98035; MJ_0055.

GeneID

1450894.

KEGG

mja:MJ_0055.

Phylogenomic databases

eggNOG

COG0108.

KO

K02858.

OMA

QMAKLIR.

ProtClustDB

CLSK876051.

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-14603.

UniPathway

UPA00275; UER00399.

Family and domain databases

Gene3D

3.90.870.10. 1 hit.

HAMAP

MF_00180. RibB.

InterPro

IPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
[Graphical view]

Pfam

PF00926. DHBP_synthase. 1 hit.
[Graphical view]

SUPFAM

SSF55821. DHBP_synth_RibB-like_a/b_dom. 1 hit.

TIGRFAMs

TIGR00506. ribB. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

Q60364.

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:	May 1, 2013
This is version 85 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program