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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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi49 – 491Zinc; catalytic
Active sitei51 – 511Proton donorBy similarity
Metal bindingi74 – 741Zinc; catalytic
Metal bindingi83 – 831Zinc; catalytic
Binding sitei153 – 1531NADP; via amide nitrogen and carbonyl oxygen
Binding sitei167 – 1671SubstrateBy similarity
Binding sitei169 – 1691NADP
Binding sitei183 – 1831SubstrateBy similarity
Binding sitei195 – 1951NADP
Binding sitei199 – 1991NADP
Binding sitei203 – 2031Substrate; via amide nitrogenBy similarity
Binding sitei206 – 2061SubstrateBy similarity
Binding sitei221 – 2211NADP
Binding sitei290 – 2901SubstrateBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi292 – 2987NADP

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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 361361Riboflavin biosynthesis protein RibDPRO_0000171715Add
BLAST

Proteomic databases

PaxDbiP17618.

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

BioGridi856545. 1 interaction.
STRINGi224308.Bsubs1_010100012781.

Structurei

Secondary structure

1
361
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi2 – 1312Combined sources
Helixi14 – 163Combined sources
Beta strandi19 – 235Combined sources
Beta strandi27 – 4115Combined sources
Helixi50 – 589Combined sources
Helixi59 – 624Combined sources
Beta strandi66 – 716Combined sources
Beta strandi78 – 803Combined sources
Helixi83 – 908Combined sources
Beta strandi94 – 996Combined sources
Turni104 – 1085Combined sources
Helixi109 – 1157Combined sources
Turni116 – 1183Combined sources
Beta strandi120 – 1234Combined sources
Helixi127 – 1337Combined sources
Helixi135 – 1439Combined sources
Beta strandi147 – 1559Combined sources
Beta strandi158 – 1614Combined sources
Helixi173 – 1797Combined sources
Helixi182 – 1854Combined sources
Beta strandi186 – 1927Combined sources
Helixi193 – 1997Combined sources
Beta strandi207 – 2093Combined sources
Beta strandi215 – 2195Combined sources
Helixi230 – 2334Combined sources
Beta strandi239 – 2435Combined sources
Helixi249 – 2568Combined sources
Turni257 – 2593Combined sources
Beta strandi261 – 2644Combined sources
Beta strandi266 – 2694Combined sources
Helixi272 – 28110Combined sources
Beta strandi286 – 2916Combined sources
Helixi293 – 30210Combined sources
Beta strandi306 – 31510Combined sources
Beta strandi320 – 3223Combined sources
Beta strandi324 – 3263Combined sources
Turni334 – 3363Combined sources
Beta strandi339 – 34810Combined sources
Beta strandi351 – 3588Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-359.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP17618.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 122122CMP/dCMP-type deaminasePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 144144DeaminaseAdd
BLAST
Regioni145 – 361217ReductaseAdd
BLAST

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
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. Positions 1-359.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi856545. 1 interaction.
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: September 7, 2016
This is version 139 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.