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Protein

Riboflavin biosynthesis protein RibD

Gene

ribD

Organism
Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / JCM 1027 / KCTC 2358 / NCIMB 9240)
Status
Unreviewed-Annotation score: -Protein inferred from homologyi

Functioni

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

Catalytic activityi

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

Cofactori

Zn2+UniRule annotationNote: Binds 1 zinc ion.UniRule annotation

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.UniRule annotation
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. GTP cyclohydrolase-2 (ribA)
  2. Riboflavin biosynthesis protein RibD (ribD)
  3. Riboflavin biosynthesis protein RibD (ribD)
  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)DescriptionActionsGraphical viewLength
Metal bindingi53Zinc; catalyticUniRule annotation1
Active sitei55Proton donorUniRule annotation1
Metal bindingi78Zinc; catalyticUniRule annotation1
Metal bindingi87Zinc; catalyticUniRule annotation1
Binding sitei157NADP; via amide nitrogen and carbonyl oxygenUniRule annotation1
Binding sitei171SubstrateUniRule annotation1
Binding sitei173NADPUniRule annotation1
Binding sitei187SubstrateUniRule annotation1
Binding sitei199NADPUniRule annotation1
Binding sitei203NADPUniRule annotation1
Binding sitei207Substrate; via amide nitrogenUniRule annotation1
Binding sitei210SubstrateUniRule annotation1
Binding sitei237NADPUniRule annotation1
Binding sitei301SubstrateUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi303 – 309NADPUniRule annotation7

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHydrolaseUniRule annotationImported, OxidoreductaseUniRule annotationImported
Biological processRiboflavin biosynthesisUniRule annotation
LigandMetal-bindingUniRule annotation, NADPUniRule annotation, ZincUniRule annotation

Enzyme and pathway databases

BioCyciAHYD380703:G1G7B-3330-MONOMER
UniPathwayi
UPA00275;UER00401

UPA00275;UER00402

Names & Taxonomyi

Protein namesi
Recommended name:
Riboflavin biosynthesis protein RibDUniRule annotation
Including the following 2 domains:
Diaminohydroxyphosphoribosylaminopyrimidine deaminaseUniRule annotation (EC:3.5.4.26UniRule annotation)
Short name:
DRAP deaminaseUniRule annotation
Alternative name(s):
Riboflavin-specific deaminaseUniRule annotation
5-amino-6-(5-phosphoribosylamino)uracil reductaseUniRule annotation (EC:1.1.1.193UniRule annotation)
Alternative name(s):
HTP reductaseUniRule annotation
Gene namesi
Name:ribDImported
Ordered Locus Names:AHA_3333Imported
OrganismiAeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / JCM 1027 / KCTC 2358 / NCIMB 9240)Imported
Taxonomic identifieri380703 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAeromonadalesAeromonadaceaeAeromonas
Proteomesi
  • UP000000756 Componenti: Chromosome

Interactioni

Protein-protein interaction databases

STRINGi380703.AHA_3333

Structurei

3D structure databases

ProteinModelPortaliA0KNH1
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini4 – 125CMP/dCMP-type deaminaseInterPro annotationAdd BLAST122

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105D1W Bacteria
COG0117 LUCA
COG1985 LUCA
HOGENOMiHOG000257442
KOiK11752
OMAiYIILKWA

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.

A0KNH1-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MFSQDDYQWM SRALELARRG RYTTAPNPCV GAVLVKAGVV VGEGWHQRAG
60 70 80 90 100
EPHAEVYALH AAGDNARGAT AYVTLEPCSH HGRTPPCAEA LIKAGVTRVV
110 120 130 140 150
AAMVDPNPQV GGRGLRMLSE AGIKTDFGLL ASEAEALNPG FFKRMRTAFP
160 170 180 190 200
QVTVKLGASL DGRTAMASGE SQWITSPEAR RDVQRLRARH DAVLSSAETV
210 220 230 240 250
LADNASLTVR WDELPASVKA SYPKETLRQP LRVIVDSQNR LTPDLPLLQS
260 270 280 290 300
EGPVLLARHK ASGEWPAWVQ QLEVPLLDGK LDLVSLFMLL AKQNVNSVLV
310 320 330 340 350
EAGPRLCGAL LDKGLVDDLV LYQAPKLMGD EGRGLFHLPG LTRLFQAPKL
360
NIKDVRMVGP DIRITARLA
Length:369
Mass (Da):40,048
Last modified:December 12, 2006 - v1
Checksum:i41B332CCDBEB4AFE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000462 Genomic DNA Translation: ABK37683.1
RefSeqiWP_011707100.1, NC_008570.1
YP_857822.1, NC_008570.1

Genome annotation databases

EnsemblBacteriaiABK37683; ABK37683; AHA_3333
GeneIDi4490113
KEGGiaha:AHA_3333
PATRICifig|380703.7.peg.3327

Similar proteinsi

Entry informationi

Entry nameiA0KNH1_AERHH
AccessioniPrimary (citable) accession number: A0KNH1
Entry historyiIntegrated into UniProtKB/TrEMBL: December 12, 2006
Last sequence update: December 12, 2006
Last modified: September 12, 2018
This is version 77 of the entry and version 1 of the sequence. See complete history.
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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