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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: 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
  1. Vmax=148 nmol/min/mg enzyme1 Publication

Pathwayi: riboflavin biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate.
Proteins known to be involved in this subpathway in this organism are:
  1. 3,4-dihydroxy-2-butanone 4-phosphate synthase (ribB)
This subpathway is part of the pathway riboflavin biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate, the pathway riboflavin biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi26Magnesium or manganese 11
Metal bindingi26Magnesium or manganese 21
Binding sitei30Substrate2 Publications1
Sitei147Essential for catalytic activity1
Metal bindingi164Magnesium or manganese 21
Binding sitei185Substrate2 Publications1
Sitei185Essential for catalytic activity1

GO - Molecular functioni

GO - Biological processi

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.
BRENDAi4.1.99.12. 3260.
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
Proteomesi
  • UP000000805 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi21D → E or N: Loss of activity. 1 Publication1
Mutagenesisi21D → S: Reduces activity 70-fold. 1 Publication1
Mutagenesisi25R → E or K: Reduces activity 50-fold. 1 Publication1
Mutagenesisi26E → D, Q or S: Loss of activity. 1 Publication1
Mutagenesisi28E → D or S: Loss of activity. 1 Publication1
Mutagenesisi28E → Q: Reduces activity 23-fold. 1 Publication1
Mutagenesisi30D → E or N: Loss of activity. 1 Publication1
Mutagenesisi30D → S: Reduces activity 30-fold. 1 Publication1
Mutagenesisi55C → G: Reduces activity 70-fold. Increases Km for ribulose-5-phosphate 7-fold. 1 Publication1
Mutagenesisi55C → S: Reduces activity 30-fold. 1 Publication1
Mutagenesisi112T → A: Reduces activity 50-fold. Increases Km for ribulose-5-phosphate 10-fold. 1 Publication1
Mutagenesisi119R → S: Reduces activity 8-fold. Increases Km for ribulose-5-phosphate 8-fold. 1 Publication1
Mutagenesisi147H → S: Reduces activity 10-fold. 1
Mutagenesisi161R → S: Reduces activity 10-fold. Increases Km for ribulose-5-phosphate 7-fold. 1 Publication1
Mutagenesisi164H → N or S: Loss of activity. 1 Publication1
Mutagenesisi165T → A: Reduces activity by 2-fold. Increases Km for ribulose-5-phosphate 8-fold. 1 Publication1
Mutagenesisi165T → S: Reduces activity by 3-fold. 1 Publication1
Mutagenesisi166E → S: Increases Km for ribulose-5-phosphate 8-fold. 1 Publication1
Mutagenesisi185E → D, Q or S: Loss of activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001518251 – 2273,4-dihydroxy-2-butanone 4-phosphate synthaseAdd BLAST227

Interactioni

Subunit structurei

Homodimer.3 Publications

Protein-protein interaction databases

STRINGi243232.MJ_0055.

Structurei

Secondary structure

1227
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 12Combined sources10
Beta strandi17 – 20Combined sources4
Turni23 – 26Combined sources4
Beta strandi29 – 34Combined sources6
Helixi35 – 37Combined sources3
Helixi40 – 49Combined sources10
Beta strandi51 – 58Combined sources8
Helixi60 – 66Combined sources7
Helixi71 – 78Combined sources8
Turni79 – 81Combined sources3
Helixi83 – 87Combined sources5
Beta strandi96 – 98Combined sources3
Beta strandi101 – 107Combined sources7
Beta strandi111 – 113Combined sources3
Helixi116 – 131Combined sources16
Helixi135 – 137Combined sources3
Helixi138 – 141Combined sources4
Beta strandi142 – 152Combined sources11
Helixi157 – 159Combined sources3
Helixi164 – 174Combined sources11
Beta strandi179 – 187Combined sources9
Beta strandi191 – 193Combined sources3
Helixi196 – 206Combined sources11
Beta strandi210 – 212Combined sources3
Helixi213 – 219Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1PVWX-ray2.45A/B/C1-227[»]
1PVYX-ray1.70A/B1-227[»]
1SNNX-ray1.55A/B1-227[»]
ProteinModelPortaliQ60364.
SMRiQ60364.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ60364.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni25 – 26Substrate binding2
Regioni161 – 165Substrate binding5

Sequence similaritiesi

Belongs to the DHBP synthase family.Curated

Phylogenomic databases

eggNOGiarCOG01320. Archaea.
COG0108. LUCA.
InParanoidiQ60364.
KOiK02858.
OMAiQMAKLIR.
PhylomeDBiQ60364.

Family and domain databases

Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00180. RibB. 1 hit.
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.
RefSeqiWP_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.
PIRiG64306.
RefSeqiWP_010869547.1. NC_000909.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1PVWX-ray2.45A/B/C1-227[»]
1PVYX-ray1.70A/B1-227[»]
1SNNX-ray1.55A/B1-227[»]
ProteinModelPortaliQ60364.
SMRiQ60364.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243232.MJ_0055.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiarCOG01320. Archaea.
COG0108. LUCA.
InParanoidiQ60364.
KOiK02858.
OMAiQMAKLIR.
PhylomeDBiQ60364.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00399.
BioCyciMetaCyc:MONOMER-14603.
BRENDAi4.1.99.12. 3260.

Miscellaneous databases

EvolutionaryTraceiQ60364.

Family and domain databases

Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00180. RibB. 1 hit.
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.
ProtoNetiSearch...

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 2, 2016
This is version 104 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.