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Q60364

- RIBB_METJA

UniProt

Q60364 - RIBB_METJA

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Protein
3,4-dihydroxy-2-butanone 4-phosphate synthase
Gene
ribB, MJ0055
Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.1 Publication

Catalytic activityi

D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate.UniRule annotation

Cofactori

Binds 2 divalent metal cations per subunit. Magnesium or manganese.1 Publication

Kineticsi

  1. KM=140 µM for ribulose-5-phosphate1 Publication

Vmax=148 nmol/min/mg enzyme

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi26 – 261Magnesium or manganese 1
Metal bindingi26 – 261Magnesium or manganese 2
Binding sitei30 – 301Substrate
Sitei147 – 1471Essential for catalytic activity
Metal bindingi164 – 1641Magnesium or manganese 2
Binding sitei185 – 1851Substrate
Sitei185 – 1851Essential for catalytic activity

GO - Molecular functioni

  1. 3,4-dihydroxy-2-butanone-4-phosphate synthase activity Source: UniProtKB-HAMAP
  2. magnesium ion binding Source: UniProtKB-HAMAP
  3. manganese ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. riboflavin biosynthetic process Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Riboflavin biosynthesis

Keywords - Ligandi

Magnesium, Manganese, Metal-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-14603.
UniPathwayiUPA00275; UER00399.

Names & Taxonomyi

Protein namesi
Recommended name:
3,4-dihydroxy-2-butanone 4-phosphate synthase (EC:4.1.99.12)
Short name:
DHBP synthase
Gene namesi
Name:ribB
Ordered Locus Names:MJ0055
OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Taxonomic identifieri243232 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
ProteomesiUP000000805: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi21 – 211D → E or N: Loss of activity. 1 Publication
Mutagenesisi21 – 211D → S: Reduces activity 70-fold. 1 Publication
Mutagenesisi25 – 251R → E or K: Reduces activity 50-fold. 1 Publication
Mutagenesisi26 – 261E → D, Q or S: Loss of activity. 1 Publication
Mutagenesisi28 – 281E → D or S: Loss of activity. 1 Publication
Mutagenesisi28 – 281E → Q: Reduces activity 23-fold. 1 Publication
Mutagenesisi30 – 301D → E or N: Loss of activity. 1 Publication
Mutagenesisi30 – 301D → S: Reduces activity 30-fold. 1 Publication
Mutagenesisi55 – 551C → G: Reduces activity 70-fold. Increases Km for ribulose-5-phosphate 7-fold. 1 Publication
Mutagenesisi55 – 551C → S: Reduces activity 30-fold. 1 Publication
Mutagenesisi112 – 1121T → A: Reduces activity 50-fold. Increases Km for ribulose-5-phosphate 10-fold. 1 Publication
Mutagenesisi119 – 1191R → S: Reduces activity 8-fold. Increases Km for ribulose-5-phosphate 8-fold. 1 Publication
Mutagenesisi147 – 1471H → S: Reduces activity 10-fold.
Mutagenesisi161 – 1611R → S: Reduces activity 10-fold. Increases Km for ribulose-5-phosphate 7-fold. 1 Publication
Mutagenesisi164 – 1641H → N or S: Loss of activity. 1 Publication
Mutagenesisi165 – 1651T → A: Reduces activity by 2-fold. Increases Km for ribulose-5-phosphate 8-fold. 1 Publication
Mutagenesisi165 – 1651T → S: Reduces activity by 3-fold. 1 Publication
Mutagenesisi166 – 1661E → S: Increases Km for ribulose-5-phosphate 8-fold. 1 Publication
Mutagenesisi185 – 1851E → D, Q or S: Loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 2272273,4-dihydroxy-2-butanone 4-phosphate synthaseUniRule annotation
PRO_0000151825Add
BLAST

Interactioni

Subunit structurei

Homodimer.3 Publications

Protein-protein interaction databases

STRINGi243232.MJ0055.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1210
Beta strandi17 – 204
Turni23 – 264
Beta strandi29 – 346
Helixi35 – 373
Helixi40 – 4910
Beta strandi51 – 588
Helixi60 – 667
Helixi71 – 788
Turni79 – 813
Helixi83 – 875
Beta strandi96 – 983
Beta strandi101 – 1077
Beta strandi111 – 1133
Helixi116 – 13116
Helixi135 – 1373
Helixi138 – 1414
Beta strandi142 – 15211
Helixi157 – 1593
Helixi164 – 17411
Beta strandi179 – 1879
Beta strandi191 – 1933
Helixi196 – 20611
Beta strandi210 – 2123
Helixi213 – 2197

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1PVWX-ray2.45A/B/C1-227[»]
1PVYX-ray1.70A/B1-227[»]
1SNNX-ray1.55A/B1-227[»]
ProteinModelPortaliQ60364.
SMRiQ60364. Positions 2-220.

Miscellaneous databases

EvolutionaryTraceiQ60364.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni25 – 262Substrate bindingUniRule annotation
Regioni161 – 1655Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the DHBP synthase family.

Phylogenomic databases

eggNOGiCOG0108.
KOiK02858.
OMAiQMAKLIR.
PhylomeDBiQ60364.

Family and domain databases

Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00180. RibB.
InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
[Graphical view]
PfamiPF00926. DHBP_synthase. 1 hit.
[Graphical view]
SUPFAMiSSF55821. SSF55821. 1 hit.
TIGRFAMsiTIGR00506. ribB. 1 hit.

Sequencei

Sequence statusi: Complete.

Q60364-1 [UniParc]FASTAAdd to Basket

« Hide

MNNVEKAIEA LKKGEIILVY DSDEREGETD MVVASQFITP EHIRIMRKDA    50
GGLICTALHP DICNKLGIPF MVDILEFASQ KFKVLRELYP NDIPYDEKSS 100
FSITINHRKT FTGITDNDRA FTIKKLAELV KEGRFNDFGK EFRSPGHVTL 150
LRAAEGLVKN RQGHTEMTVA LAELANLVPI TTICEMMGDD GNAMSKNETK 200
RYAEKHNLIY LSGEEIINYY LDKYLKD 227
Length:227
Mass (Da):25,797
Last modified:November 1, 1997 - v1
Checksum:i0718EE5B4247995D
GO

Mass spectrometryi

Molecular mass is 25799 Da from positions 1 - 227. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
L77117 Genomic DNA. Translation: AAB98035.1.
PIRiG64306.
RefSeqiNP_247019.1. NC_000909.1.
WP_010869547.1. NC_000909.1.

Genome annotation databases

EnsemblBacteriaiAAB98035; AAB98035; MJ_0055.
GeneIDi1450894.
KEGGimja:MJ_0055.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
L77117 Genomic DNA. Translation: AAB98035.1 .
PIRi G64306.
RefSeqi NP_247019.1. NC_000909.1.
WP_010869547.1. NC_000909.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 [» ]
ProteinModelPortali Q60364.
SMRi Q60364. Positions 2-220.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 243232.MJ0055.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAB98035 ; AAB98035 ; MJ_0055 .
GeneIDi 1450894.
KEGGi mja:MJ_0055.

Phylogenomic databases

eggNOGi COG0108.
KOi K02858.
OMAi QMAKLIR.
PhylomeDBi Q60364.

Enzyme and pathway databases

UniPathwayi UPA00275 ; UER00399 .
BioCyci MetaCyc:MONOMER-14603.

Miscellaneous databases

EvolutionaryTracei Q60364.

Family and domain databases

Gene3Di 3.90.870.10. 1 hit.
HAMAPi MF_00180. RibB.
InterProi IPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
[Graphical view ]
Pfami PF00926. DHBP_synthase. 1 hit.
[Graphical view ]
SUPFAMi SSF55821. SSF55821. 1 hit.
TIGRFAMsi TIGR00506. ribB. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. 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.

Entry informationi

Entry nameiRIBB_METJA
AccessioniPrimary (citable) accession number: Q60364
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: September 3, 2014
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Methanococcus jannaschii
    Methanococcus jannaschii: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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