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Protein

Riboflavin biosynthesis protein RibD

Gene

ribD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)-pyrimidinedione 5'-phosphate.

Catalytic activityi

2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H2O = 5-amino-6-(5-phosphoribosylamino)uracil + NH3.
5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP+ = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH.

Cofactori

Zn2+1 PublicationNote: Binds 1 zinc ion.1 Publication

Pathwayi: riboflavin biosynthesis

This protein is involved in step 2 and 3 of the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP.
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 (ribD)
  3. Riboflavin biosynthesis protein RibD (ribD)
  4. 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YwtE (ywtE), 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YcsE (ycsE), 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YitU (yitU)
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 bindingi49Zinc; catalytic1
Active sitei51Proton donorBy similarity1
Metal bindingi74Zinc; catalytic1
Metal bindingi83Zinc; catalytic1
Binding sitei153NADP; via amide nitrogen and carbonyl oxygen1
Binding sitei167SubstrateBy similarity1
Binding sitei169NADP1
Binding sitei183SubstrateBy similarity1
Binding sitei195NADP1
Binding sitei199NADP1
Binding sitei203Substrate; via amide nitrogenBy similarity1
Binding sitei206SubstrateBy similarity1
Binding sitei221NADP1
Binding sitei290SubstrateBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi292 – 298NADP7

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHydrolase, Multifunctional enzyme, Oxidoreductase
Biological processRiboflavin biosynthesis
LigandMetal-binding, NADP, Zinc

Enzyme and pathway databases

BioCyciBSUB:BSU23280-MONOMER
BRENDAi1.1.1.193 658
UniPathwayi
UPA00275;UER00401

UPA00275;UER00402

Names & Taxonomyi

Protein namesi
Recommended name:
Riboflavin biosynthesis protein RibD
Including the following 2 domains:
Diaminohydroxyphosphoribosylaminopyrimidine deaminase (EC:3.5.4.26)
Short name:
DRAP deaminase
Alternative name(s):
Riboflavin-specific deaminase
5-amino-6-(5-phosphoribosylamino)uracil reductase (EC:1.1.1.193)
Alternative name(s):
HTP reductase
Gene namesi
Name:ribD
Synonyms:ribG
Ordered Locus Names:BSU23280
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001717151 – 361Riboflavin biosynthesis protein RibDAdd BLAST361

Proteomic databases

PaxDbiP17618
PRIDEiP17618

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

BioGridi856545, 1 interactor
STRINGi224308.Bsubs1_010100012781

Structurei

Secondary structure

1361
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP17618
SMRiP17618
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP17618

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 122CMP/dCMP-type deaminasePROSITE-ProRule annotationAdd BLAST122

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 144DeaminaseAdd BLAST144
Regioni145 – 361ReductaseAdd BLAST217

Sequence similaritiesi

In the N-terminal section; belongs to the cytidine and deoxycytidylate deaminase family.Curated
In the C-terminal section; belongs to the HTP reductase family.Curated

Phylogenomic databases

eggNOGiENOG4105D1W Bacteria
COG0117 LUCA
COG1985 LUCA
HOGENOMiHOG000257443
InParanoidiP17618
KOiK11752
OMAiYIILKWA
PhylomeDBiP17618

Family and domain databases

Gene3Di3.40.430.10, 1 hit
InterProiView protein in InterPro
IPR016192 APOBEC/CMP_deaminase_Zn-bd
IPR002125 CMP_dCMP_dom
IPR016193 Cytidine_deaminase-like
IPR024072 DHFR-like_dom_sf
IPR004794 Eubact_RibD
IPR011549 RibD_C
IPR002734 RibDG_C
PfamiView protein in Pfam
PF00383 dCMP_cyt_deam_1, 1 hit
PF01872 RibD_C, 1 hit
PIRSFiPIRSF006769 RibD, 1 hit
SUPFAMiSSF53597 SSF53597, 1 hit
SSF53927 SSF53927, 1 hit
TIGRFAMsiTIGR00326 eubact_ribD, 1 hit
TIGR00227 ribD_Cterm, 1 hit
PROSITEiView protein in PROSITE
PS00903 CYT_DCMP_DEAMINASES_1, 1 hit
PS51747 CYT_DCMP_DEAMINASES_2, 1 hit

Sequencei

Sequence statusi: Complete.

P17618-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MEEYYMKLAL DLAKQGEGQT ESNPLVGAVV VKDGQIVGMG AHLKYGEAHA
60 70 80 90 100
EVHAIHMAGA HAEGADIYVT LEPCSHYGKT PPCAELIINS GIKRVFVAMR
110 120 130 140 150
DPNPLVAGRG ISMMKEAGIE VREGILADQA ERLNEKFLHF MRTGLPYVTL
160 170 180 190 200
KAAASLDGKI ATSTGDSKWI TSEAARQDAQ QYRKTHQSIL VGVGTVKADN
210 220 230 240 250
PSLTCRLPNV TKQPVRVILD TVLSIPEDAK VICDQIAPTW IFTTARADEE
260 270 280 290 300
KKKRLSAFGV NIFTLETERI QIPDVLKILA EEGIMSVYVE GGSAVHGSFV
310 320 330 340 350
KEGCFQEIIF YFAPKLIGGT HAPSLISGEG FQSMKDVPLL QFTDITQIGR
360
DIKLTAKPTK E
Length:361
Mass (Da):39,305
Last modified:August 1, 1990 - v1
Checksum:iDA836930BFDECA3B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X51510 Genomic DNA Translation: CAA35878.1
L09228 Genomic DNA Translation: AAA67481.1
AL009126 Genomic DNA Translation: CAB14260.1
PIRiS45543 PN0100
RefSeqiNP_390209.1, NC_000964.3
WP_004398763.1, NZ_JNCM01000036.1

Genome annotation databases

EnsemblBacteriaiCAB14260; CAB14260; BSU23280
GeneIDi938945
KEGGibsu:BSU23280
PATRICifig|224308.179.peg.2535

Similar proteinsi

Entry informationi

Entry nameiRIBD_BACSU
AccessioniPrimary (citable) accession number: P17618
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: August 1, 1990
Last modified: May 23, 2018
This is version 148 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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