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Protein

GTP cyclohydrolase 1 type 2 homolog

Gene

ybgI

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Provides significant protection from radiation damage and may be involved in the degradation of radiation-damaged nucleotides.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi63 – 631Divalent metal cation 11 Publication
Metal bindingi64 – 641Divalent metal cation 21 Publication
Metal bindingi101 – 1011Divalent metal cation 11 Publication
Metal bindingi215 – 2151Divalent metal cation 21 Publication
Metal bindingi219 – 2191Divalent metal cation 11 Publication
Metal bindingi219 – 2191Divalent metal cation 21 Publication

GO - Molecular functioni

  • identical protein binding Source: EcoCyc
  • metal ion binding Source: EcoCyc

GO - Biological processi

  • DNA repair Source: UniProtKB-KW
  • response to ionizing radiation Source: EcoCyc
Complete GO annotation...

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G6379-MONOMER.
ECOL316407:JW0700-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
GTP cyclohydrolase 1 type 2 homologCurated
Alternative name(s):
Radiation resistance protein YbgI1 Publication
Gene namesi
Name:ybgI
Ordered Locus Names:b0710, JW0700
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13305. ybgI.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene show a 2-3 orders of magnitude drop in survival after exposure to ionizing radiation as compared to a wild-type strain.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 247247GTP cyclohydrolase 1 type 2 homologPRO_0000147307Add
BLAST

Proteomic databases

EPDiP0AFP6.
PaxDbiP0AFP6.
PRIDEiP0AFP6.

Interactioni

Subunit structurei

Toroid-shaped homohexamer. In the hexamer, 3 dimers assemble to form a ring-like structure surrounding a central hole.1 Publication

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4259921. 135 interactions.
DIPiDIP-36185N.
IntActiP0AFP6. 6 interactions.
MINTiMINT-1276952.
STRINGi511145.b0710.

Structurei

Secondary structure

1
247
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1311Combined sources
Beta strandi26 – 294Combined sources
Beta strandi37 – 437Combined sources
Helixi46 – 549Combined sources
Beta strandi58 – 647Combined sources
Helixi78 – 8811Combined sources
Beta strandi92 – 954Combined sources
Helixi98 – 1025Combined sources
Turni104 – 1063Combined sources
Helixi108 – 1169Combined sources
Beta strandi118 – 1258Combined sources
Beta strandi128 – 13710Combined sources
Helixi139 – 15012Combined sources
Beta strandi155 – 1573Combined sources
Beta strandi163 – 1708Combined sources
Beta strandi172 – 1743Combined sources
Helixi176 – 1783Combined sources
Helixi179 – 1857Combined sources
Beta strandi188 – 1936Combined sources
Helixi197 – 2059Combined sources
Beta strandi209 – 2124Combined sources
Helixi215 – 2184Combined sources
Helixi221 – 23313Combined sources
Beta strandi237 – 2404Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NMOX-ray2.20A/B/C/D/E/F1-247[»]
1NMPX-ray2.20A/B/C/D/E/F1-247[»]
ProteinModelPortaliP0AFP6.
SMRiP0AFP6. Positions 1-247.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AFP6.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4107QNR. Bacteria.
COG0327. LUCA.
HOGENOMiHOG000014258.
InParanoidiP0AFP6.
OMAiRVGWCTG.
OrthoDBiEOG6N3CRB.
PhylomeDBiP0AFP6.

Family and domain databases

InterProiIPR002678. GTP_cyclohydrolase_I/Nif3.
[Graphical view]
PANTHERiPTHR13799. PTHR13799. 1 hit.
PfamiPF01784. NIF3. 1 hit.
[Graphical view]
SUPFAMiSSF102705. SSF102705. 1 hit.
TIGRFAMsiTIGR00486. YbgI_SA1388. 1 hit.

Sequencei

Sequence statusi: Complete.

P0AFP6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKNTELEQLI NEKLNSAAIS DYAPNGLQVE GKETVQKIVT GVTASQALLD
60 70 80 90 100
EAVRLGADAV IVHHGYFWKG ESPVIRGMKR NRLKTLLAND INLYGWHLPL
110 120 130 140 150
DAHPELGNNA QLAALLGITV MGEIEPLVPW GELTMPVPGL ELASWIEARL
160 170 180 190 200
GRKPLWCGDT GPEVVQRVAW CTGGGQSFID SAARFGVDAF ITGEVSEQTI
210 220 230 240
HSAREQGLHF YAAGHHATER GGIRALSEWL NENTDLDVTF IDIPNPA
Length:247
Mass (Da):26,892
Last modified:December 20, 2005 - v1
Checksum:i07436A9E410DF007
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC73804.1.
AP009048 Genomic DNA. Translation: BAA35374.1.
PIRiE64806.
RefSeqiNP_415238.1. NC_000913.3.
WP_000798871.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73804; AAC73804; b0710.
BAA35374; BAA35374; BAA35374.
GeneIDi945824.
KEGGiecj:JW0700.
eco:b0710.
PATRICi32116615. VBIEscCol129921_0740.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC73804.1.
AP009048 Genomic DNA. Translation: BAA35374.1.
PIRiE64806.
RefSeqiNP_415238.1. NC_000913.3.
WP_000798871.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NMOX-ray2.20A/B/C/D/E/F1-247[»]
1NMPX-ray2.20A/B/C/D/E/F1-247[»]
ProteinModelPortaliP0AFP6.
SMRiP0AFP6. Positions 1-247.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259921. 135 interactions.
DIPiDIP-36185N.
IntActiP0AFP6. 6 interactions.
MINTiMINT-1276952.
STRINGi511145.b0710.

Proteomic databases

EPDiP0AFP6.
PaxDbiP0AFP6.
PRIDEiP0AFP6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73804; AAC73804; b0710.
BAA35374; BAA35374; BAA35374.
GeneIDi945824.
KEGGiecj:JW0700.
eco:b0710.
PATRICi32116615. VBIEscCol129921_0740.

Organism-specific databases

EchoBASEiEB3089.
EcoGeneiEG13305. ybgI.

Phylogenomic databases

eggNOGiENOG4107QNR. Bacteria.
COG0327. LUCA.
HOGENOMiHOG000014258.
InParanoidiP0AFP6.
OMAiRVGWCTG.
OrthoDBiEOG6N3CRB.
PhylomeDBiP0AFP6.

Enzyme and pathway databases

BioCyciEcoCyc:G6379-MONOMER.
ECOL316407:JW0700-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0AFP6.
PROiP0AFP6.

Family and domain databases

InterProiIPR002678. GTP_cyclohydrolase_I/Nif3.
[Graphical view]
PANTHERiPTHR13799. PTHR13799. 1 hit.
PfamiPF01784. NIF3. 1 hit.
[Graphical view]
SUPFAMiSSF102705. SSF102705. 1 hit.
TIGRFAMsiTIGR00486. YbgI_SA1388. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Escherichia coli genes and pathways involved in surviving extreme exposure to ionizing radiation."
    Byrne R.T., Chen S.H., Wood E.A., Cabot E.L., Cox M.M.
    J. Bacteriol. 196:3534-3545(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.
    Strain: K12.
  5. "Crystal structure of Escherichia coli protein ybgI, a toroidal structure with a dinuclear metal site."
    Ladner J.E., Obmolova G., Teplyakov A., Howard A.J., Khil P.P., Camerini-Otero R.D., Gilliland G.L.
    BMC Struct. Biol. 3:7-7(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH METAL IONS, SUBUNIT.

Entry informationi

Entry nameiGCH1L_ECOLI
AccessioniPrimary (citable) accession number: P0AFP6
Secondary accession number(s): P75743
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: April 13, 2016
This is version 84 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, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.