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Protein

Riboflavin biosynthesis protein RibD

Gene

ribD

Organism
Acinetobacter baumannii ATCC 19606 = CIP 70.34
Status
Unreviewed-Annotation score: Annotation score: 2 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

Pathway:iriboflavin 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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi54 – 541Zinc; via pros nitrogenCombined sources
Metal bindingi79 – 791ZincCombined sources
Metal bindingi88 – 881ZincCombined sources

GO - Molecular functioni

GO - Biological processi

Keywords - Molecular functioni

HydrolaseUniRule annotationImported, OxidoreductaseUniRule annotationImported

Keywords - Biological processi

Riboflavin biosynthesisUniRule annotation

Keywords - Ligandi

Metal-bindingCombined sources, NADPUniRule annotation, ZincCombined sources

Enzyme and pathway databases

BRENDAi1.1.1.193. 98.
UniPathwayiUPA00275; UER00401.
UPA00275; UER00402.

Names & Taxonomyi

Protein namesi
Recommended name:
Riboflavin biosynthesis protein RibDUniRule annotation
Gene namesi
Name:ribDImported
ORF Names:F911_03682Imported, HMPREF0010_02004Imported
OrganismiAcinetobacter baumannii ATCC 19606 = CIP 70.34Imported
Taxonomic identifieri575584 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesMoraxellaceaeAcinetobacterAcinetobacter calcoaceticus/baumannii complex

Interactioni

Protein-protein interaction databases

STRINGi575584.HMPREF0010_02004.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3ZPCX-ray2.20A/B1-361[»]
3ZPGX-ray1.99A1-361[»]
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

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

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.

D0CB74-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSELKQDQYW MQQAIELAKR GLYSTKPNPN VGCVIVKDDQ LIGEGFHPKA
60 70 80 90 100
GQPHAEVFAL RQAGEQAQGA TAYVTLEPCA HYGRTPPCAE ALVKAQVKKV
110 120 130 140 150
VVACPDPNPL VAGKGVQILK NAGIEVEIGI CEDLAAKLNQ GFLKAMSTGM
160 170 180 190 200
PYVRLKVASS LDGRTAMASG ESKWITGSAA RQDVQHWRAI SGAVITGIDT
210 220 230 240 250
VIADDCQLNV RSLHNIDIET VAQPKRVILD RRGRLPLTAK ILENPETVMV
260 270 280 290 300
MGPYRQELAD LGVIQLEIQP LKTLLQTLSK QYQIYDVLIE AGATLSSAFL
310 320 330 340 350
QEGLIDEMIS YVAPTLLGQS ARAMFNADFE YMAQQLRFKL LDVIQLDQDI
360
RLRLIPTQEK V
Length:361
Mass (Da):39,633
Last modified:November 24, 2009 - v1
Checksum:i13F6A01D4B132ACA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
GG704574 Genomic DNA. Translation: EEX03756.1.
APRG01000018 Genomic DNA. Translation: ENW73393.1.
RefSeqiWP_001292503.1. NZ_KL810966.1.

Genome annotation databases

EnsemblBacteriaiEEX03756; EEX03756; HMPREF0010_02004.
ENW73393; ENW73393; F911_03682.
KFC02170; KFC02170; DJ41_1419.
PATRICi24333545. VBIAciBau3967_1967.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
GG704574 Genomic DNA. Translation: EEX03756.1.
APRG01000018 Genomic DNA. Translation: ENW73393.1.
RefSeqiWP_001292503.1. NZ_KL810966.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3ZPCX-ray2.20A/B1-361[»]
3ZPGX-ray1.99A1-361[»]
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi575584.HMPREF0010_02004.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiEEX03756; EEX03756; HMPREF0010_02004.
ENW73393; ENW73393; F911_03682.
KFC02170; KFC02170; DJ41_1419.
PATRICi24333545. VBIAciBau3967_1967.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00401.
UPA00275; UER00402.
BRENDAi1.1.1.193. 98.

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...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE.
    Strain: ATCC 19606Imported.
  2. "Structure of diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase from Acinetobacter baumannii."
    Dawson A., Trumper P., Chrysostomou G., Hunter W.N.
    Acta Crystallogr. F 69:611-617(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.99 ANGSTROMS) IN COMPLEX WITH ZINC.
  3. Cited for: NUCLEOTIDE SEQUENCE.
    Strain: CIP 70.34Imported.

Entry informationi

Entry nameiD0CB74_ACIBA
AccessioniPrimary (citable) accession number: D0CB74
Entry historyi
Integrated into UniProtKB/TrEMBL: November 24, 2009
Last sequence update: November 24, 2009
Last modified: June 24, 2015
This is version 40 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources

External Data

Dasty 3

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 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.