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Protein

Putative acid--amine ligase YgiC

Gene

ygiC

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

May be a ligase forming an amide bond. Shows ATPase activity. Despite its similarity to the C-terminal synthetase domain of Gss, is not a glutathionylspermidine (Gsp) synthetase. Cannot synthesize Gsp, glutathione (GSH), or GSH intermediates, from GSH and spermidine, cysteine and glutamate, gamma-glutamylcysteine and spermidine, and gamma-glutamylcysteine and glycine. Does not bind to Gsp.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei100 – 1001Transition state stabilizerBy similarity
Metal bindingi102 – 1021Magnesium 1By similarity
Metal bindingi115 – 1151Magnesium 1By similarity
Metal bindingi115 – 1151Magnesium 2By similarity
Metal bindingi117 – 1171Magnesium 2By similarity
Binding sitei267 – 2671ATPBy similarity
Binding sitei302 – 3021ATPBy similarity
Binding sitei309 – 3091ATP; via amide nitrogenBy similarity
Binding sitei336 – 3361ATPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi100 – 1023ATPBy similarity
Nucleotide bindingi371 – 3733ATPBy similarity

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11165-MONOMER.
ECOL316407:JW3006-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Putative acid--amine ligase YgiC (EC:6.3.1.-)
Gene namesi
Name:ygiC
Ordered Locus Names:b3038, JW3006
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11165. ygiC.

Pathology & Biotechi

Disruption phenotypei

Deletion of this gene does not affect the ability to synthesize glutathionylspermidine. There is no visible differences between wild-type and mutant strain growth in LB media.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 386386Putative acid--amine ligase YgiCPRO_0000169401Add
BLAST

Proteomic databases

PaxDbiP0ADT5.
PRIDEiP0ADT5.

Interactioni

Protein-protein interaction databases

BioGridi4262389. 16 interactions.
DIPiDIP-48176N.
IntActiP0ADT5. 13 interactions.
MINTiMINT-1290041.
STRINGi511145.b3038.

Structurei

3D structure databases

ProteinModelPortaliP0ADT5.
SMRiP0ADT5. Positions 37-386.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4106032. Bacteria.
COG0754. LUCA.
HOGENOMiHOG000249104.
InParanoidiP0ADT5.
OMAiWSEEAYY.
OrthoDBiEOG66XB93.
PhylomeDBiP0ADT5.

Family and domain databases

InterProiIPR005494. GSPS_pre-ATP-grasp-like_dom.
IPR016185. PreATP-grasp_dom.
[Graphical view]
PfamiPF03738. GSP_synth. 1 hit.
[Graphical view]
SUPFAMiSSF52440. SSF52440. 1 hit.

Sequencei

Sequence statusi: Complete.

P0ADT5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MERVSITERP DWREKAHEYG FNFHTMYGEP YWCEDAYYKL TLAQVEKLEE
60 70 80 90 100
VTAELHQMCL KVVEKVIASD ELMTKFRIPK HTWSFVRQSW LTHQPSLYSR
110 120 130 140 150
LDLAWDGTGE PKLLENNADT PTSLYEAAFF QWIWLEDQLN AGNLPEGSDQ
160 170 180 190 200
FNSLQEKLID RFVELREQYG FQLLHLTCCR DTVEDRGTIQ YLQDCATEAE
210 220 230 240 250
IATEFLYIDD IGLGEKGQFT DLQDQVISNL FKLYPWEFML REMFSTKLED
260 270 280 290 300
AGVRWLEPAW KSIISNKALL PLLWEMFPNH PNLLPAYFAE DDHPQMEKYV
310 320 330 340 350
VKPIFSREGA NVSIIENGKT IEAAEGPYGE EGMIVQQFHP LPKFGDSYML
360 370 380
IGSWLVNDQP AGIGIREDRA LITQDMSRFY PHIFVE
Length:386
Mass (Da):45,026
Last modified:December 6, 2005 - v1
Checksum:i5DB19CE4F3FE4783
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M77129 Genomic DNA. Translation: AAA71876.1.
U28377 Genomic DNA. Translation: AAA69206.1.
U00096 Genomic DNA. Translation: AAC76074.1.
AP009048 Genomic DNA. Translation: BAE77094.1.
PIRiS22361.
RefSeqiNP_417510.1. NC_000913.3.
WP_000442860.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76074; AAC76074; b3038.
BAE77094; BAE77094; BAE77094.
GeneIDi947249.
KEGGiecj:JW3006.
eco:b3038.
PATRICi32121486. VBIEscCol129921_3130.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M77129 Genomic DNA. Translation: AAA71876.1.
U28377 Genomic DNA. Translation: AAA69206.1.
U00096 Genomic DNA. Translation: AAC76074.1.
AP009048 Genomic DNA. Translation: BAE77094.1.
PIRiS22361.
RefSeqiNP_417510.1. NC_000913.3.
WP_000442860.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP0ADT5.
SMRiP0ADT5. Positions 37-386.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262389. 16 interactions.
DIPiDIP-48176N.
IntActiP0ADT5. 13 interactions.
MINTiMINT-1290041.
STRINGi511145.b3038.

Proteomic databases

PaxDbiP0ADT5.
PRIDEiP0ADT5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76074; AAC76074; b3038.
BAE77094; BAE77094; BAE77094.
GeneIDi947249.
KEGGiecj:JW3006.
eco:b3038.
PATRICi32121486. VBIEscCol129921_3130.

Organism-specific databases

EchoBASEiEB1153.
EcoGeneiEG11165. ygiC.

Phylogenomic databases

eggNOGiENOG4106032. Bacteria.
COG0754. LUCA.
HOGENOMiHOG000249104.
InParanoidiP0ADT5.
OMAiWSEEAYY.
OrthoDBiEOG66XB93.
PhylomeDBiP0ADT5.

Enzyme and pathway databases

BioCyciEcoCyc:EG11165-MONOMER.
ECOL316407:JW3006-MONOMER.

Miscellaneous databases

PROiP0ADT5.

Family and domain databases

InterProiIPR005494. GSPS_pre-ATP-grasp-like_dom.
IPR016185. PreATP-grasp_dom.
[Graphical view]
PfamiPF03738. GSP_synth. 1 hit.
[Graphical view]
SUPFAMiSSF52440. SSF52440. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence of a region duplicated in Escherichia coli toc mutants."
    Yang T.-P., Depew R.E.
    Biochim. Biophys. Acta 1130:227-228(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  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. "Comparison of the functions of glutathionylspermidine synthetase/amidase from E. coli and its predicted homologues YgiC and YjfC."
    Sui L., Warren J.C., Russell J.P., Stourman N.V.
    Int. J. Biochem. Mol. Biol. 3:302-312(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: LACK OF GLUTATHIONYLSPERMIDINE SYNTHETASE ACTIVITY, FUNCTION, ATP-BINDING, DISRUPTION PHENOTYPE.
    Strain: K12.

Entry informationi

Entry nameiYGIC_ECOLI
AccessioniPrimary (citable) accession number: P0ADT5
Secondary accession number(s): P24196, Q2M9G2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: December 6, 2005
Last modified: January 20, 2016
This is version 76 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

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. 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.