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UniProtKB - D2RNY5 (D2RNY5_ACIFV)

UniProt

D2RNY5 - D2RNY5_ACIFV

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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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi32 – 321Magnesium or manganese 1UniRule annotation
Metal bindingi32 – 321Magnesium or manganese 2UniRule annotation
Binding sitei36 – 361D-ribulose 5-phosphateUniRule annotation
Sitei129 – 1291Essential for DHBP synthase activityUniRule annotation
Metal bindingi146 – 1461Magnesium or manganese 2UniRule annotation
Binding sitei167 – 1671D-ribulose 5-phosphateUniRule annotation
Sitei167 – 1671Essential for DHBP synthase activityUniRule annotation
Metal bindingi260 – 2601Zinc; catalyticUniRule annotation
Metal bindingi271 – 2711Zinc; catalyticUniRule annotation
Metal bindingi273 – 2731Zinc; catalyticUniRule annotation
Binding sitei276 – 2761GTPUniRule annotation
Binding sitei320 – 3201GTPUniRule annotation
Active sitei332 – 3321Proton acceptor; for GTP cyclohydrolase activityUniRule annotation
Active sitei334 – 3341Nucleophile; for GTP cyclohydrolase activityUniRule annotation
Binding sitei355 – 3551GTPUniRule annotation
Binding sitei360 – 3601GTPUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi255 – 2595GTPUniRule annotation
Nucleotide bindingi298 – 3003GTPUniRule annotation

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

BioCyciAFER591001:GHUL-373-MONOMER.
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 lineageiBacteria › Firmicutes › Negativicutes › Acidaminococcales › Acidaminococcaceae › Acidaminococcus ›
Proteomesi
  • UP000001902 Componenti: Chromosome

Interactioni

Protein-protein interaction databases

STRINGi591001.Acfer_0355.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini211 – 376166GTP_cyclohydro2InterPro annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 204204DHBP synthaseUniRule annotationAdd
BLAST
Regioni31 – 322D-ribulose 5-phosphate bindingUniRule annotation
Regioni143 – 1475D-ribulose 5-phosphate bindingUniRule annotation
Regioni205 – 408204GTP cyclohydrolase IIUniRule annotationAdd
BLAST

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.
BioCyciAFER591001:GHUL-373-MONOMER.

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: September 7, 2016
This is version 50 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.