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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

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.

Cofactori

Mg2+1 Publication, Mn2+1 PublicationNote: 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 enzyme1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi26 – 261Magnesium or manganese 1
Metal bindingi26 – 261Magnesium or manganese 2
Binding sitei30 – 301Substrate2 Publications
Sitei147 – 1471Essential for catalytic activity
Metal bindingi164 – 1641Magnesium or manganese 2
Binding sitei185 – 1851Substrate2 Publications
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 synthasePRO_0000151825Add
BLAST

Interactioni

Subunit structurei

Homodimer.3 Publications

Protein-protein interaction databases

STRINGi243232.MJ0055.

Structurei

Secondary structure

1
227
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1210Combined sources
Beta strandi17 – 204Combined sources
Turni23 – 264Combined sources
Beta strandi29 – 346Combined sources
Helixi35 – 373Combined sources
Helixi40 – 4910Combined sources
Beta strandi51 – 588Combined sources
Helixi60 – 667Combined sources
Helixi71 – 788Combined sources
Turni79 – 813Combined sources
Helixi83 – 875Combined sources
Beta strandi96 – 983Combined sources
Beta strandi101 – 1077Combined sources
Beta strandi111 – 1133Combined sources
Helixi116 – 13116Combined sources
Helixi135 – 1373Combined sources
Helixi138 – 1414Combined sources
Beta strandi142 – 15211Combined sources
Helixi157 – 1593Combined sources
Helixi164 – 17411Combined sources
Beta strandi179 – 1879Combined sources
Beta strandi191 – 1933Combined sources
Helixi196 – 20611Combined sources
Beta strandi210 – 2123Combined sources
Helixi213 – 2197Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ60364.

Family & Domainsi

Region

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

Sequence similaritiesi

Belongs to the DHBP synthase family.Curated

Phylogenomic databases

eggNOGiCOG0108.
InParanoidiQ60364.
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

        10         20         30         40         50
MNNVEKAIEA LKKGEIILVY DSDEREGETD MVVASQFITP EHIRIMRKDA
60 70 80 90 100
GGLICTALHP DICNKLGIPF MVDILEFASQ KFKVLRELYP NDIPYDEKSS
110 120 130 140 150
FSITINHRKT FTGITDNDRA FTIKKLAELV KEGRFNDFGK EFRSPGHVTL
160 170 180 190 200
LRAAEGLVKN RQGHTEMTVA LAELANLVPI TTICEMMGDD GNAMSKNETK
210 220
RYAEKHNLIY LSGEEIINYY LDKYLKD
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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.
InParanoidi Q60364.
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: November 26, 2014
This is version 93 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