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Protein

3,4-dihydroxy-2-butanone 4-phosphate synthase

Gene

RIB3

Organism
Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)
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.By similarity

Catalytic activityi

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

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 2 divalent metal cations per subunit. Magnesium or manganese.By similarity

Kineticsi

  1. KM=37 µM for ribulose-5-phosphate1 Publication
  1. Vmax=332 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 (RIB3)
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 bindingi30Magnesium or manganese 1By similarity1
Metal bindingi30Magnesium or manganese 2By similarity1
Binding sitei34Substrate1 Publication1
Sitei128Essential for catalytic activityBy similarity1
Metal bindingi145Magnesium or manganese 2By similarity1
Binding sitei166SubstrateBy similarity1
Sitei166Essential 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

BRENDAi4.1.99.12. 1096.
SABIO-RKQ5A3V6.
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:RIB3
ORF Names:CaO19.12693, CaO19.5228
OrganismiCandida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)
Taxonomic identifieri237561 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesDebaryomycetaceaeCandida/Lodderomyces cladeCandida
Proteomesi
  • UP000000559 Componenti: Unassembled WGS sequence

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi59C → A: Increases Km for substrate 18-fold. Reduces activity by 30%. 1
Mutagenesisi87Y → A: Increases Km for substrate 4-fold. Reduces activity by 98%. 1 Publication1
Mutagenesisi92D → A: Loss of activity. Alters protein folding and stability. 1 Publication1
Mutagenesisi166E → A: Loss of activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002966851 – 2043,4-dihydroxy-2-butanone 4-phosphate synthaseAdd BLAST204

Proteomic databases

PRIDEiQ5A3V6.

Interactioni

Subunit structurei

Homodimer.1 Publication

Structurei

Secondary structure

1204
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi8 – 16Combined sources9
Beta strandi21 – 27Combined sources7
Beta strandi34 – 38Combined sources5
Helixi39 – 41Combined sources3
Helixi44 – 52Combined sources9
Beta strandi59 – 63Combined sources5
Helixi64 – 69Combined sources6
Beta strandi91 – 94Combined sources4
Beta strandi98 – 100Combined sources3
Helixi103 – 114Combined sources12
Helixi120 – 122Combined sources3
Beta strandi123 – 134Combined sources12
Helixi138 – 140Combined sources3
Helixi145 – 155Combined sources11
Beta strandi160 – 168Combined sources9
Turni170 – 172Combined sources3
Helixi178 – 188Combined sources11
Beta strandi192 – 194Combined sources3
Helixi195 – 202Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TKSX-ray1.60A/B1-204[»]
1TKUX-ray1.66A/B1-204[»]
2RISX-ray1.60A1-204[»]
2RIUX-ray1.70A1-204[»]
ProteinModelPortaliQ5A3V6.
SMRiQ5A3V6.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5A3V6.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni29 – 30Substrate bindingBy similarity2
Regioni142 – 146Substrate binding5

Sequence similaritiesi

Belongs to the DHBP synthase family.Curated

Phylogenomic databases

InParanoidiQ5A3V6.
KOiK02858.
OrthoDBiEOG092C42BA.

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.

Q5A3V6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTNIFTPIEE ALEAYKNGEF LIVMDDEDRE NEGDLIMAAE LITQEKMAFL
60 70 80 90 100
VRYSSGYVCV PLSEERANQL ELPPMLANRS DRHGTAYTIT CDFAEGTTTG
110 120 130 140 150
ISAHDRALTT RSLANPNSKP QDFIKPGHIL PLRAVPGLLK KRRGHTEAAV
160 170 180 190 200
QLSTLAGLQP AGVICELVRD EDGLMMRLDD CIQFGKKHGI KIININQLVE

YISK
Length:204
Mass (Da):22,658
Last modified:July 24, 2007 - v2
Checksum:i5FEC62C3ABDA822E
GO

Sequence cautioni

The sequence EAK97301 differs from that shown. Reason: Frameshift at position 117.Curated
The sequence EAK97301 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence EAK97363 differs from that shown. Reason: Erroneous initiation.Curated

Mass spectrometryi

Molecular mass is 22530 Da from positions 2 - 204. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AACQ01000070 Genomic DNA. Translation: EAK97363.1. Different initiation.
AACQ01000071 Genomic DNA. Translation: EAK97301.1. Sequence problems.
RefSeqiXP_716297.1. XM_711204.1.
XP_716359.1. XM_711266.1.

Genome annotation databases

EnsemblFungiiEAK97301; EAK97301; CaO19.5228.
EAK97363; EAK97363; CaO19.12693.
GeneIDi3641955.
3642062.
KEGGical:CaO19.12693.
cal:CaO19.5228.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AACQ01000070 Genomic DNA. Translation: EAK97363.1. Different initiation.
AACQ01000071 Genomic DNA. Translation: EAK97301.1. Sequence problems.
RefSeqiXP_716297.1. XM_711204.1.
XP_716359.1. XM_711266.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TKSX-ray1.60A/B1-204[»]
1TKUX-ray1.66A/B1-204[»]
2RISX-ray1.60A1-204[»]
2RIUX-ray1.70A1-204[»]
ProteinModelPortaliQ5A3V6.
SMRiQ5A3V6.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiQ5A3V6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiEAK97301; EAK97301; CaO19.5228.
EAK97363; EAK97363; CaO19.12693.
GeneIDi3641955.
3642062.
KEGGical:CaO19.12693.
cal:CaO19.5228.

Phylogenomic databases

InParanoidiQ5A3V6.
KOiK02858.
OrthoDBiEOG092C42BA.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00399.
BRENDAi4.1.99.12. 1096.
SABIO-RKQ5A3V6.

Miscellaneous databases

EvolutionaryTraceiQ5A3V6.

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 nameiRIB3_CANAL
AccessioniPrimary (citable) accession number: Q5A3V6
Secondary accession number(s): Q5A3P2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 24, 2007
Last sequence update: July 24, 2007
Last modified: November 2, 2016
This is version 77 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

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

Documents

  1. Candida albicans
    Candida albicans: 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.