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Protein

Riboflavin biosynthesis protein RibD

Gene

TM_1828

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Status
Unreviewed-Annotation score: Annotation score: 3 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.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. Riboflavin biosynthesis protein RibBA (Tmari_1836), Riboflavin biosynthesis protein RibBA (ribBA)
  2. Riboflavin biosynthesis protein RibD (TM_1828)
  3. Riboflavin biosynthesis protein RibD (TM_1828)
  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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi49 – 491Zinc; catalyticUniRule annotation
Metal bindingi49 – 491Zinc; via pros nitrogenCombined sources
Active sitei51 – 511Proton donorUniRule annotation
Metal bindingi77 – 771ZincCombined sources
Metal bindingi77 – 771Zinc; catalyticUniRule annotation
Metal bindingi86 – 861ZincCombined sources
Metal bindingi86 – 861Zinc; catalyticUniRule annotation
Binding sitei155 – 1551NADP; via amide nitrogen and carbonyl oxygenUniRule annotationCombined sources
Binding sitei162 – 1621NADP; via carbonyl oxygenCombined sources
Binding sitei169 – 1691SubstrateUniRule annotation
Binding sitei171 – 1711NADPUniRule annotation
Binding sitei184 – 1841SubstrateUniRule annotation
Binding sitei196 – 1961NADPUniRule annotation
Binding sitei200 – 2001NADPUniRule annotationCombined sources
Binding sitei204 – 2041Substrate; via amide nitrogenUniRule annotation
Binding sitei207 – 2071SubstrateUniRule annotation
Binding sitei261 – 2611NADP; via carbonyl oxygenCombined sources
Binding sitei281 – 2811SubstrateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi167 – 1693NADPCombined sources
Nucleotide bindingi195 – 1962NADPCombined sources
Nucleotide bindingi219 – 2213NADPCombined sources
Nucleotide bindingi283 – 2897NADPUniRule annotationCombined sources

GO - Molecular functioni

GO - Biological processi

Keywords - Molecular functioni

HydrolaseUniRule annotationImported, OxidoreductaseUniRule annotationImported

Keywords - Biological processi

Riboflavin biosynthesisUniRule annotation

Keywords - Ligandi

Metal-bindingUniRule annotationCombined sources, NADPUniRule annotationCombined sources, Nucleotide-bindingCombined sources, ZincUniRule annotationCombined sources

Enzyme and pathway databases

BioCyciTMAR243274:GC6P-1879-MONOMER.
UniPathwayiUPA00275; UER00401.
UPA00275; UER00402.

Names & Taxonomyi

Protein namesi
Recommended name:
Riboflavin biosynthesis protein RibDUniRule annotation
Gene namesi
Ordered Locus Names:TM_1828Imported
ORF Names:Tmari_1838Imported
OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Imported
Taxonomic identifieri243274 [NCBI]
Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
Proteomesi
  • UP000013901 Componenti: Chromosome
  • UP000008183 Componenti: Chromosome

Interactioni

Protein-protein interaction databases

STRINGi243274.TM1828.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2HXVX-ray1.80A1-348[»]
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 124124CMP/dCMP-type deaminaseInterPro annotationAdd
BLAST

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.
KOiK11752.
OMAiHWGKQPP.
OrthoDBiEOG66F07R.

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.
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.
PROSITEiPS00903. CYT_DCMP_DEAMINASES_1. 1 hit.
PS51747. CYT_DCMP_DEAMINASES_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9X2E8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYETFMKRAI ELAKKGLGRV NPNPPVGAVV VKDGRIIAEG FHPYFGGPHA
60 70 80 90 100
ERMAIESARK KGEDLRGATL IVTLEPCDHH GKTPPCTDLI IESGIKTVVI
110 120 130 140 150
GTRDPNPVSG NGVEKFRNHG IEVIEGVLEE EVKKLCEFFI TYVTKKRPFV
160 170 180 190 200
ALKYASTLDG KIADHRGDSK WITDKLRFKV HEMRNIYSAV LVGAGTVLKD
210 220 230 240 250
NPQLTCRLKE GRNPVRVILD RKGVLSGKVF RVFEENARVI VFTESEEAEY
260 270 280 290 300
PPHVEKALSD CSVESILRNL YERDIDSVLV EGGSKVFSEF LDHADVVFGF
310 320 330 340
YSTKIFGKGL DVFSGYLSDV SVPPKFKVVN VEFSDSEFLV EMRPCSRE
Length:348
Mass (Da):38,866
Last modified:November 1, 1999 - v1
Checksum:i7E2BC27F08D33FDF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD36891.1.
CP004077 Genomic DNA. Translation: AGL50762.1.
PIRiG72207.
RefSeqiNP_229625.1. NC_000853.1.
WP_004082374.1. NZ_CP011107.1.

Genome annotation databases

EnsemblBacteriaiAAD36891; AAD36891; TM_1828.
AGL50762; AGL50762; Tmari_1838.
GeneIDi897425.
KEGGitma:TM1828.
tmi:THEMA_05055.
tmm:Tmari_1838.
tmw:THMA_1873.
PATRICi23938643. VBITheMar51294_1848.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD36891.1.
CP004077 Genomic DNA. Translation: AGL50762.1.
PIRiG72207.
RefSeqiNP_229625.1. NC_000853.1.
WP_004082374.1. NZ_CP011107.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2HXVX-ray1.80A1-348[»]
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243274.TM1828.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD36891; AAD36891; TM_1828.
AGL50762; AGL50762; Tmari_1838.
GeneIDi897425.
KEGGitma:TM1828.
tmi:THEMA_05055.
tmm:Tmari_1838.
tmw:THMA_1873.
PATRICi23938643. VBITheMar51294_1848.

Phylogenomic databases

eggNOGiENOG4105D1W. Bacteria.
COG0117. LUCA.
COG1985. LUCA.
KOiK11752.
OMAiHWGKQPP.
OrthoDBiEOG66F07R.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00401.
UPA00275; UER00402.
BioCyciTMAR243274:GC6P-1879-MONOMER.

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.
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.
PROSITEiPS00903. CYT_DCMP_DEAMINASES_1. 1 hit.
PS51747. CYT_DCMP_DEAMINASES_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099Imported and MSB8Imported.
  2. "The genome organization of Thermotoga maritima reflects its lifestyle."
    Latif H., Lerman J.A., Portnoy V.A., Tarasova Y., Nagarajan H., Schrimpe-Rutledge A.C., Smith R.D., Adkins J.N., Lee D.H., Qiu Y., Zengler K.
    PLoS Genet. 9:E1003485-E1003485(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099Imported and MSB8Imported.

Entry informationi

Entry nameiQ9X2E8_THEMA
AccessioniPrimary (citable) accession number: Q9X2E8
Secondary accession number(s): G4FGL5
Entry historyi
Integrated into UniProtKB/TrEMBL: November 1, 1999
Last sequence update: November 1, 1999
Last modified: March 16, 2016
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources, Complete proteome, Reference proteomeImported

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.