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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: 4 out of 5- Protein inferred from homologyi

Display
All None

  • Function
  • Names & Taxonomy
  • Subcellular locationSubcell. location
  • Pathology & BiotechPathol./Biotech
  • PTM / Processing
  • Expression
  • Interaction
  • Structure
  • Family & Domains
  • Sequence
  • Cross-references
  • Publications
  • Entry information
  • Miscellaneous
  • Similar proteins
Top

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 annotationSAAS 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 annotation

Cofactori

Protein has several cofactor binding sites:
  • Mg2+UniRule annotation, Mn2+UniRule annotationNote: Binds 2 divalent metal cations per subunit. Magnesium or manganese.UniRule annotation
  • Zn2+UniRule annotationNote: Binds 1 zinc ion per subunit.UniRule annotation

Pathwayi

Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1.
Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-ribitylamino)uracil from GTP: step 1/4.

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

  1. 3,4-dihydroxy-2-butanone-4-phosphate synthase activity Source: UniProtKB-HAMAP
  2. GTP binding Source: UniProtKB-KW
  3. GTP cyclohydrolase II activity Source: UniProtKB-HAMAP
  4. magnesium ion binding Source: UniProtKB-HAMAP
  5. manganese ion binding Source: UniProtKB-HAMAP
  6. zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. riboflavin biosynthetic process Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

HydrolaseUniRule annotation, LyaseUniRule 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 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 › Selenomonadales › Acidaminococcaceae › Acidaminococcus ›
ProteomesiUP000001902: Chromosome

Family & Domainsi

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 annotation
In the N-terminal section; belongs to the DHBP synthase family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000115440.
KOiK14652.
OMAiLMVDRNT.

Family and domain databases

Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00179. RibA.
MF_00180. RibB.
MF_01283. RibBA.
InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
IPR000926. GTP_CycHdrlaseII_RibA.
IPR016299. Riboflavin_synth_RibBA.
[Graphical view]
PfamiPF00926. DHBP_synthase. 1 hit.
PF00925. GTP_cyclohydro2. 1 hit.
[Graphical view]
PIRSFiPIRSF001259. RibA. 1 hit.
SUPFAMiSSF55821. 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.
RefSeqiYP_003398076.1. NC_013740.1.

Genome annotation databases

EnsemblBacteriaiADB46761; ADB46761; Acfer_0355.
GeneIDi8736803.
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 .
RefSeqi YP_003398076.1. NC_013740.1.

3D structure databases

ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ADB46761 ; ADB46761 ; Acfer_0355 .
GeneIDi 8736803.
KEGGi afn:Acfer_0355.
PATRICi 31907259. VBIAciFer109666_0376.

Phylogenomic databases

HOGENOMi HOG000115440.
KOi K14652.
OMAi LMVDRNT.

Enzyme and pathway databases

UniPathwayi UPA00275 ; UER00399 .
UPA00275 ; UER00400 .
BioCyci AFER591001:GHUL-373-MONOMER.

Family and domain databases

Gene3Di 3.90.870.10. 1 hit.
HAMAPi MF_00179. RibA.
MF_00180. RibB.
MF_01283. RibBA.
InterProi IPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
IPR000926. GTP_CycHdrlaseII_RibA.
IPR016299. Riboflavin_synth_RibBA.
[Graphical view ]
Pfami PF00926. DHBP_synthase. 1 hit.
PF00925. GTP_cyclohydro2. 1 hit.
[Graphical view ]
PIRSFi PIRSF001259. RibA. 1 hit.
SUPFAMi SSF55821. SSF55821. 1 hit.
TIGRFAMsi TIGR00505. ribA. 1 hit.
TIGR00506. ribB. 1 hit.
ProtoNeti Search...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 25085 / DSM 20731 / VR4Imported.

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: January 7, 2015
This is version 34 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

External Data

Dasty 3

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 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.
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