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Protein

Riboflavin biosynthesis protein RibD

Gene

ribD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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 YitU (yitU), 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YwtE (ywtE), 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YcsE (ycsE)
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

Keywords - Molecular functioni

Hydrolase, Oxidoreductase

Keywords - Biological processi

Riboflavin biosynthesis

Keywords - Ligandi

Metal-binding, NADP, Zinc

Enzyme and pathway databases

BioCyciBSUB:BSU23280-MONOMER.
BRENDAi1.1.1.193. 658.
UniPathwayiUPA00275; 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

Subcellular locationi

GO - Cellular componenti

PTM / Processingi

Molecule processing

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

Proteomic databases

PaxDbiP17618.

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
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi2 – 13Combined sources12
Helixi14 – 16Combined sources3
Beta strandi19 – 23Combined sources5
Beta strandi27 – 41Combined sources15
Helixi50 – 58Combined sources9
Helixi59 – 62Combined sources4
Beta strandi66 – 71Combined sources6
Beta strandi78 – 80Combined sources3
Helixi83 – 90Combined sources8
Beta strandi94 – 99Combined sources6
Turni104 – 108Combined sources5
Helixi109 – 115Combined sources7
Turni116 – 118Combined sources3
Beta strandi120 – 123Combined sources4
Helixi127 – 133Combined sources7
Helixi135 – 143Combined sources9
Beta strandi147 – 155Combined sources9
Beta strandi158 – 161Combined sources4
Helixi173 – 179Combined sources7
Helixi182 – 185Combined sources4
Beta strandi186 – 192Combined sources7
Helixi193 – 199Combined sources7
Beta strandi207 – 209Combined sources3
Beta strandi215 – 219Combined sources5
Helixi230 – 233Combined sources4
Beta strandi239 – 243Combined sources5
Helixi249 – 256Combined sources8
Turni257 – 259Combined sources3
Beta strandi261 – 264Combined sources4
Beta strandi266 – 269Combined sources4
Helixi272 – 281Combined sources10
Beta strandi286 – 291Combined sources6
Helixi293 – 302Combined sources10
Beta strandi306 – 315Combined sources10
Beta strandi320 – 322Combined sources3
Beta strandi324 – 326Combined sources3
Turni334 – 336Combined sources3
Beta strandi339 – 348Combined sources10
Beta strandi351 – 358Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2B3ZX-ray2.41A/B/C/D1-361[»]
2D5NX-ray2.97A/B/C/D1-361[»]
3EX8X-ray2.56A/B/C/D1-361[»]
4G3MX-ray2.56A/B/C/D1-361[»]
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
Contains 1 CMP/dCMP-type deaminase domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4105D1W. Bacteria.
COG0117. LUCA.
COG1985. LUCA.
HOGENOMiHOG000257443.
InParanoidiP17618.
KOiK11752.
OMAiGHRWRAR.
PhylomeDBiP17618.

Family and domain databases

Gene3Di3.40.430.10. 1 hit.
InterProiIPR016192. APOBEC/CMP_deaminase_Zn-bd.
IPR002125. CMP_dCMP_Zn-bd.
IPR016193. Cytidine_deaminase-like.
IPR024072. DHFR-like_dom.
IPR004794. Eubact_RibD.
IPR011549. RibD_C.
IPR002734. RibDG_C.
[Graphical view]
PfamiPF00383. dCMP_cyt_deam_1. 1 hit.
PF01872. RibD_C. 1 hit.
[Graphical view]
PIRSFiPIRSF006769. RibD. 1 hit.
SUPFAMiSSF53597. SSF53597. 1 hit.
SSF53927. SSF53927. 1 hit.
TIGRFAMsiTIGR00326. eubact_ribD. 1 hit.
TIGR00227. ribD_Cterm. 1 hit.
PROSITEiPS00903. CYT_DCMP_DEAMINASES_1. 1 hit.
PS51747. CYT_DCMP_DEAMINASES_2. 1 hit.
[Graphical view]

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.
PATRICi18976473. VBIBacSub10457_2427.

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2B3ZX-ray2.41A/B/C/D1-361[»]
2D5NX-ray2.97A/B/C/D1-361[»]
3EX8X-ray2.56A/B/C/D1-361[»]
4G3MX-ray2.56A/B/C/D1-361[»]
ProteinModelPortaliP17618.
SMRiP17618.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi856545. 1 interactor.
STRINGi224308.Bsubs1_010100012781.

Proteomic databases

PaxDbiP17618.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB14260; CAB14260; BSU23280.
GeneIDi938945.
KEGGibsu:BSU23280.
PATRICi18976473. VBIBacSub10457_2427.

Phylogenomic databases

eggNOGiENOG4105D1W. Bacteria.
COG0117. LUCA.
COG1985. LUCA.
HOGENOMiHOG000257443.
InParanoidiP17618.
KOiK11752.
OMAiGHRWRAR.
PhylomeDBiP17618.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00401.
UPA00275; UER00402.
BioCyciBSUB:BSU23280-MONOMER.
BRENDAi1.1.1.193. 658.

Miscellaneous databases

EvolutionaryTraceiP17618.

Family and domain databases

Gene3Di3.40.430.10. 1 hit.
InterProiIPR016192. APOBEC/CMP_deaminase_Zn-bd.
IPR002125. CMP_dCMP_Zn-bd.
IPR016193. Cytidine_deaminase-like.
IPR024072. DHFR-like_dom.
IPR004794. Eubact_RibD.
IPR011549. RibD_C.
IPR002734. RibDG_C.
[Graphical view]
PfamiPF00383. dCMP_cyt_deam_1. 1 hit.
PF01872. RibD_C. 1 hit.
[Graphical view]
PIRSFiPIRSF006769. RibD. 1 hit.
SUPFAMiSSF53597. SSF53597. 1 hit.
SSF53927. SSF53927. 1 hit.
TIGRFAMsiTIGR00326. eubact_ribD. 1 hit.
TIGR00227. ribD_Cterm. 1 hit.
PROSITEiPS00903. CYT_DCMP_DEAMINASES_1. 1 hit.
PS51747. CYT_DCMP_DEAMINASES_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRIBD_BACSU
AccessioniPrimary (citable) accession number: P17618
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: August 1, 1990
Last modified: November 2, 2016
This is version 141 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  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.