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Q60364 (RIBB_METJA) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 87. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) [Reference proteome] [HAMAP]
Taxonomic identifier243232 [NCBI]
Taxonomic lineageArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus

Protein attributes

Sequence length227 AA.
Sequence statusComplete.
Protein existenceEvidence 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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 2272273,4-dihydroxy-2-butanone 4-phosphate synthase HAMAP-Rule MF_00180
PRO_0000151825

Regions

Region25 – 262Substrate binding HAMAP-Rule MF_00180
Region161 – 1655Substrate binding HAMAP-Rule MF_00180

Sites

Metal binding261Magnesium or manganese 1
Metal binding261Magnesium or manganese 2
Metal binding1641Magnesium or manganese 2
Binding site301Substrate
Binding site1851Substrate
Site1471Essential for catalytic activity
Site1851Essential for catalytic activity

Experimental info

Mutagenesis211D → E or N: Loss of activity. Ref.2
Mutagenesis211D → S: Reduces activity 70-fold. Ref.2
Mutagenesis251R → E or K: Reduces activity 50-fold. Ref.2
Mutagenesis261E → D, Q or S: Loss of activity. Ref.2
Mutagenesis281E → D or S: Loss of activity. Ref.2
Mutagenesis281E → Q: Reduces activity 23-fold. Ref.2
Mutagenesis301D → E or N: Loss of activity. Ref.2
Mutagenesis301D → S: Reduces activity 30-fold. Ref.2
Mutagenesis551C → G: Reduces activity 70-fold. Increases Km for ribulose-5-phosphate 7-fold. Ref.2
Mutagenesis551C → S: Reduces activity 30-fold. Ref.2
Mutagenesis1121T → A: Reduces activity 50-fold. Increases Km for ribulose-5-phosphate 10-fold. Ref.2
Mutagenesis1191R → S: Reduces activity 8-fold. Increases Km for ribulose-5-phosphate 8-fold. Ref.2
Mutagenesis1471H → S: Reduces activity 10-fold.
Mutagenesis1611R → S: Reduces activity 10-fold. Increases Km for ribulose-5-phosphate 7-fold. Ref.2
Mutagenesis1641H → N or S: Loss of activity. Ref.2
Mutagenesis1651T → A: Reduces activity by 2-fold. Increases Km for ribulose-5-phosphate 8-fold. Ref.2
Mutagenesis1651T → S: Reduces activity by 3-fold. Ref.2
Mutagenesis1661E → S: Increases Km for ribulose-5-phosphate 8-fold. Ref.2
Mutagenesis1851E → D, Q or S: Loss of activity. Ref.2

Secondary structure

.............................................. 227
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q60364 [UniParc].

Last modified November 1, 1997. Version 1.
Checksum: 0718EE5B4247995D

FASTA22725,797
        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 

« Hide

References

« Hide '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. expand/collapse author list , 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.
PIRG64306.
RefSeqNP_247019.1. NC_000909.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1PVWX-ray2.45A/B/C1-227[»]
1PVYX-ray1.70A/B1-227[»]
1SNNX-ray1.55A/B1-227[»]
ProteinModelPortalQ60364.
SMRQ60364. Positions 2-220.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING243232.MJ0055.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAB98035; AAB98035; MJ_0055.
GeneID1450894.
KEGGmja:MJ_0055.

Phylogenomic databases

eggNOGCOG0108.
KOK02858.
OMAQMAKLIR.
ProtClustDBCLSK876051.

Enzyme and pathway databases

BioCycMetaCyc:MONOMER-14603.
UniPathwayUPA00275; UER00399.

Family and domain databases

Gene3D3.90.870.10. 1 hit.
HAMAPMF_00180. RibB.
InterProIPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
[Graphical view]
PfamPF00926. DHBP_synthase. 1 hit.
[Graphical view]
SUPFAMSSF55821. SSF55821. 1 hit.
TIGRFAMsTIGR00506. ribB. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ60364.

Entry information

Entry nameRIBB_METJA
AccessionPrimary (citable) accession number: Q60364
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: February 19, 2014
This is version 87 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Methanococcus jannaschii

Methanococcus jannaschii: entries and gene names