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Protein

Riboflavin biosynthesis protein RibBA

Gene

ribBA

Organism
Acidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / VR4)
Status
Unreviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.UniRule annotationSAAS annotation
Catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and pyrophosphate.UniRule annotation

Catalytic activityi

D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate.UniRule annotation
GTP + 3 H2O = formate + 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine + diphosphate.UniRule annotationSAAS annotation

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotationNote: Binds 2 divalent metal cations per subunit. Magnesium or manganese.UniRule annotation

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.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Riboflavin biosynthesis protein RibBA (ribBA)
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.

Pathwayi: riboflavin biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP.SAAS annotation
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. Riboflavin biosynthesis protein RibBA (ribBA)
  2. Riboflavin biosynthesis protein RibD (Acfer_0353)
  3. Riboflavin biosynthesis protein RibD (Acfer_0353)
  4. no protein annotated in this organism
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 5-amino-6-(D-ribitylamino)uracil from GTP, the pathway riboflavin biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi32Magnesium or manganese 1UniRule annotation1
Metal bindingi32Magnesium or manganese 2UniRule annotation1
Binding sitei36D-ribulose 5-phosphateUniRule annotation1
Sitei129Essential for DHBP synthase activityUniRule annotation1
Metal bindingi146Magnesium or manganese 2UniRule annotation1
Binding sitei167D-ribulose 5-phosphateUniRule annotation1
Sitei167Essential for DHBP synthase activityUniRule annotation1
Metal bindingi260Zinc; catalyticUniRule annotation1
Metal bindingi271Zinc; catalyticUniRule annotation1
Metal bindingi273Zinc; catalyticUniRule annotation1
Binding sitei276GTPUniRule annotation1
Binding sitei320GTPUniRule annotation1
Active sitei332Proton acceptor; for GTP cyclohydrolase activityUniRule annotation1
Active sitei334Nucleophile; for GTP cyclohydrolase activityUniRule annotation1
Binding sitei355GTPUniRule annotation1
Binding sitei360GTPUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi255 – 259GTPUniRule annotation5
Nucleotide bindingi298 – 300GTPUniRule annotation3

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

HydrolaseUniRule annotation, LyaseUniRule annotationSAAS annotation

Keywords - Biological processi

Riboflavin biosynthesisUniRule annotationSAAS annotation

Keywords - Ligandi

GTP-bindingUniRule annotationSAAS annotation, MagnesiumUniRule annotation, ManganeseUniRule annotation, Metal-bindingUniRule annotationSAAS annotation, Nucleotide-binding, ZincUniRule annotationSAAS annotation

Enzyme and pathway databases

UniPathwayiUPA00275; UER00399.
UPA00275; UER00400.

Names & Taxonomyi

Protein namesi
Recommended name:
Riboflavin biosynthesis protein RibBAUniRule annotationSAAS annotation
Gene namesi
Name:ribBAUniRule annotation
Ordered Locus Names:Acfer_0355Imported
OrganismiAcidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / VR4)Imported
Taxonomic identifieri591001 [NCBI]
Taxonomic lineageiBacteriaFirmicutesNegativicutesAcidaminococcalesAcidaminococcaceaeAcidaminococcus
Proteomesi
  • UP000001902 Componenti: Chromosome

Interactioni

Protein-protein interaction databases

STRINGi591001.Acfer_0355.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini211 – 376GTP_cyclohydro2InterPro annotationAdd BLAST166

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 204DHBP synthaseUniRule annotationAdd BLAST204
Regioni31 – 32D-ribulose 5-phosphate bindingUniRule annotation2
Regioni143 – 147D-ribulose 5-phosphate bindingUniRule annotation5
Regioni205 – 408GTP cyclohydrolase IIUniRule annotationAdd BLAST204

Sequence similaritiesi

In the C-terminal section; belongs to the GTP cyclohydrolase II family.UniRule annotationSAAS annotation
In the N-terminal section; belongs to the DHBP synthase family.UniRule annotationSAAS annotation

Phylogenomic databases

eggNOGiENOG4105C66. Bacteria.
COG0108. LUCA.
COG0807. LUCA.
HOGENOMiHOG000115440.
KOiK14652.
OMAiLMVDRNT.
OrthoDBiPOG091H008U.

Family and domain databases

CDDicd00641. GTP_cyclohydro2. 1 hit.
Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00179. RibA. 1 hit.
MF_00180. RibB. 1 hit.
MF_01283. RibBA. 1 hit.
InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
IPR032677. GTP_cyclohydro_II.
IPR000926. RibA.
IPR016299. Riboflavin_synth_RibBA.
[Graphical view]
PfamiPF00926. DHBP_synthase. 1 hit.
PF00925. GTP_cyclohydro2. 1 hit.
[Graphical view]
SUPFAMiSSF142695. SSF142695. 1 hit.
SSF55821. SSF55821. 1 hit.
TIGRFAMsiTIGR00505. ribA. 1 hit.
TIGR00506. ribB. 1 hit.

Sequencei

Sequence statusi: Complete.

D2RNY5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDKKFQFAPI EQAIEDIRAG KMVLVTDDPD RENEGDLIMS AEYVTPDDIN
60 70 80 90 100
FMATHAKGLI CMPCDGAILD RLQMEPMVAN NTDNHETAFT VSIDHKDTTT
110 120 130 140 150
GISAVERAYT IKKCTDESAK PEDFRRPGHV FPLRSREGGV LRRTGHTETT
160 170 180 190 200
TDLCRLAGLK PVGICCEIMS ADGTMARTPE LIEFARKFNL TFITVADLIA
210 220 230 240 250
YRKKNEKMVH RIANVALPSK YGTFRAIGYE NDLDDKCHVA IIKGDVAGKK
260 270 280 290 300
DVLVRVHSEC LTGDALGSLR CDCGDQLATS LKMIEKEGCG VVLYMQQEGR
310 320 330 340 350
GIGLANKLRA YELQDQGLDT VDANVKLGFK PDMRDYGIGA QILADLGLTS
360 370 380 390 400
IRLMTNNPAK RAGLSGYGIT ITETVPIIMK DNCYNHRYMV TKQVRMGHEL

HEDVEDAK
Length:408
Mass (Da):45,199
Last modified:March 2, 2010 - v1
Checksum:iE9C03148F8FE9109
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001859 Genomic DNA. Translation: ADB46761.1.
RefSeqiWP_012937751.1. NC_013740.1.

Genome annotation databases

EnsemblBacteriaiADB46761; ADB46761; Acfer_0355.
KEGGiafn:Acfer_0355.
PATRICi31907259. VBIAciFer109666_0376.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001859 Genomic DNA. Translation: ADB46761.1.
RefSeqiWP_012937751.1. NC_013740.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi591001.Acfer_0355.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADB46761; ADB46761; Acfer_0355.
KEGGiafn:Acfer_0355.
PATRICi31907259. VBIAciFer109666_0376.

Phylogenomic databases

eggNOGiENOG4105C66. Bacteria.
COG0108. LUCA.
COG0807. LUCA.
HOGENOMiHOG000115440.
KOiK14652.
OMAiLMVDRNT.
OrthoDBiPOG091H008U.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00399.
UPA00275; UER00400.

Family and domain databases

CDDicd00641. GTP_cyclohydro2. 1 hit.
Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00179. RibA. 1 hit.
MF_00180. RibB. 1 hit.
MF_01283. RibBA. 1 hit.
InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
IPR032677. GTP_cyclohydro_II.
IPR000926. RibA.
IPR016299. Riboflavin_synth_RibBA.
[Graphical view]
PfamiPF00926. DHBP_synthase. 1 hit.
PF00925. GTP_cyclohydro2. 1 hit.
[Graphical view]
SUPFAMiSSF142695. SSF142695. 1 hit.
SSF55821. SSF55821. 1 hit.
TIGRFAMsiTIGR00505. ribA. 1 hit.
TIGR00506. ribB. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiD2RNY5_ACIFV
AccessioniPrimary (citable) accession number: D2RNY5
Entry historyi
Integrated into UniProtKB/TrEMBL: March 2, 2010
Last sequence update: March 2, 2010
Last modified: November 30, 2016
This is version 53 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Multifunctional enzymeUniRule annotation, Reference proteomeImported

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.