Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Riboflavin biosynthesis protein RibD

Gene

ribD

Organism
Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
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. 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 bindingi54Zinc; catalyticUniRule annotation1
Metal bindingi54Zinc; via pros nitrogenCombined sources1
Active sitei56Proton donorUniRule annotation1
Metal bindingi79ZincCombined sources1
Metal bindingi79Zinc; catalyticUniRule annotation1
Metal bindingi88ZincCombined sources1
Metal bindingi88Zinc; catalyticUniRule annotation1
Binding sitei158NADP; via amide nitrogen and carbonyl oxygenUniRule annotation1
Binding sitei172SubstrateUniRule annotation1
Binding sitei174NADPUniRule annotation1
Binding sitei188SubstrateUniRule annotation1
Binding sitei200NADPUniRule annotation1
Binding sitei204NADPUniRule annotation1
Binding sitei208Substrate; via amide nitrogenUniRule annotation1
Binding sitei211SubstrateUniRule annotation1
Binding sitei290SubstrateUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi292 – 298NADPUniRule annotation7

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 annotation, ZincUniRule annotationCombined 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 70.34 = JCM 6841Imported
Taxonomic identifieri575584 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesMoraxellaceaeAcinetobacterAcinetobacter calcoaceticus/baumannii complex
Proteomesi
  • UP000013132 Componenti: Unassembled WGS sequence
  • UP000005740 Componenti: Unassembled WGS sequence

Interactioni

Protein-protein interaction databases

STRINGi575584.HMPREF0010_02004.

Structurei

3D structure databases

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

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini5 – 127CMP/dCMP-type deaminaseInterPro annotationAdd BLAST123

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.

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.
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
PDB 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.
PATRICi24333545. VBIAciBau3967_1967.

Phylogenomic databases

eggNOGiENOG4105D1W. Bacteria.
COG0117. LUCA.
COG1985. LUCA.

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...

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: July 6, 2016
This is version 47 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources, Complete 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.