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Protein

tRNA-modifying protein YgfZ

Gene

ygfZ

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

Functioni

Folate-binding protein involved in regulating the level of ATP-DnaA and in the modification of some tRNAs. It is probably a key factor in regulatory networks that act via tRNA modification, such as initiation of chromosomal replication.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei27FolateSequence analysis1
Binding sitei189FolateSequence analysis1

GO - Molecular functioni

  • folic acid binding Source: EcoCyc

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

Folate-binding

Enzyme and pathway databases

BioCyciEcoCyc:G7511-MONOMER.
ECOL316407:JW2866-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA-modifying protein YgfZ
Gene namesi
Name:ygfZ
Synonyms:yzzW
Ordered Locus Names:b2898, JW2866
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12685. ygfZ.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001698342 – 326tRNA-modifying protein YgfZAdd BLAST325

Proteomic databases

EPDiP0ADE8.
PaxDbiP0ADE8.
PRIDEiP0ADE8.

2D gel databases

SWISS-2DPAGEP0ADE8.

Interactioni

Protein-protein interaction databases

BioGridi4261457. 783 interactors.
DIPiDIP-48117N.
IntActiP0ADE8. 6 interactors.
MINTiMINT-1257340.
STRINGi511145.b2898.

Structurei

Secondary structure

1326
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi14 – 16Combined sources3
Beta strandi19 – 23Combined sources5
Beta strandi27 – 34Combined sources8
Helixi37 – 42Combined sources6
Beta strandi45 – 47Combined sources3
Helixi49 – 51Combined sources3
Beta strandi57 – 63Combined sources7
Beta strandi69 – 78Combined sources10
Beta strandi81 – 87Combined sources7
Helixi88 – 99Combined sources12
Beta strandi103 – 106Combined sources4
Beta strandi108 – 112Combined sources5
Beta strandi114 – 122Combined sources9
Helixi125 – 130Combined sources6
Beta strandi139 – 141Combined sources3
Beta strandi143 – 146Combined sources4
Beta strandi149 – 154Combined sources6
Beta strandi156 – 158Combined sources3
Beta strandi160 – 165Combined sources6
Helixi167 – 177Combined sources11
Turni178 – 180Combined sources3
Beta strandi181 – 184Combined sources4
Helixi186 – 196Combined sources11
Helixi203 – 205Combined sources3
Helixi211 – 214Combined sources4
Helixi216 – 218Combined sources3
Beta strandi224 – 226Combined sources3
Helixi232 – 237Combined sources6
Beta strandi246 – 253Combined sources8
Beta strandi265 – 269Combined sources5
Beta strandi272 – 276Combined sources5
Beta strandi278 – 284Combined sources7
Beta strandi290 – 297Combined sources8
Beta strandi306 – 308Combined sources3
Beta strandi315 – 318Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NRKX-ray2.80A1-325[»]
1VLYX-ray1.30A1-326[»]
ProteinModelPortaliP0ADE8.
SMRiP0ADE8.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0ADE8.

Family & Domainsi

Sequence similaritiesi

Belongs to the tRNA-modifying YgfZ family.Curated

Phylogenomic databases

eggNOGiENOG4106XY2. Bacteria.
COG0354. LUCA.
HOGENOMiHOG000261300.
InParanoidiP0ADE8.
KOiK06980.
OMAiGRMQSSF.
PhylomeDBiP0ADE8.

Family and domain databases

HAMAPiMF_01175. tRNA_modifying_YgfZ. 1 hit.
InterProiIPR006222. GCV_T_N.
IPR029043. GcvT/YgfZ_C.
IPR023758. tRNA-modifying_YgfZ.
IPR017703. YgfZ/GcvT_CS.
[Graphical view]
PfamiPF01571. GCV_T. 1 hit.
[Graphical view]
SUPFAMiSSF101790. SSF101790. 1 hit.
TIGRFAMsiTIGR03317. ygfZ_signature. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0ADE8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAFTPFPPRQ PTASARLPLT LMTLDDWALA TITGADSEKY MQGQVTADVS
60 70 80 90 100
QMAEDQHLLA AHCDAKGKMW SNLRLFRDGD GFAWIERRSV REPQLTELKK
110 120 130 140 150
YAVFSKVTIA PDDERVLLGV AGFQARAALA NLFSELPSKE KQVVKEGATT
160 170 180 190 200
LLWFEHPAER FLIVTDEATA NMLTDKLRGE AELNNSQQWL ALNIEAGFPV
210 220 230 240 250
IDAANSGQFI PQATNLQALG GISFKKGCYT GQEMVARAKF RGANKRALWL
260 270 280 290 300
LAGSASRLPE AGEDLELKMG ENWRRTGTVL AAVKLEDGQV VVQVVMNNDM
310 320
EPDSIFRVRD DANTLHIEPL PYSLEE
Length:326
Mass (Da):36,094
Last modified:January 23, 2007 - v2
Checksum:i08E050CE26B56B77
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti8P → D AA sequence (PubMed:9298646).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U28375 Genomic DNA. Translation: AAA83079.1.
U00096 Genomic DNA. Translation: AAC75936.1.
AP009048 Genomic DNA. Translation: BAE76963.1.
PIRiB65074.
RefSeqiNP_417374.1. NC_000913.3.
WP_000886062.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75936; AAC75936; b2898.
BAE76963; BAE76963; BAE76963.
GeneIDi947384.
KEGGiecj:JW2866.
eco:b2898.
PATRICi32121210. VBIEscCol129921_2993.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U28375 Genomic DNA. Translation: AAA83079.1.
U00096 Genomic DNA. Translation: AAC75936.1.
AP009048 Genomic DNA. Translation: BAE76963.1.
PIRiB65074.
RefSeqiNP_417374.1. NC_000913.3.
WP_000886062.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NRKX-ray2.80A1-325[»]
1VLYX-ray1.30A1-326[»]
ProteinModelPortaliP0ADE8.
SMRiP0ADE8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261457. 783 interactors.
DIPiDIP-48117N.
IntActiP0ADE8. 6 interactors.
MINTiMINT-1257340.
STRINGi511145.b2898.

2D gel databases

SWISS-2DPAGEP0ADE8.

Proteomic databases

EPDiP0ADE8.
PaxDbiP0ADE8.
PRIDEiP0ADE8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75936; AAC75936; b2898.
BAE76963; BAE76963; BAE76963.
GeneIDi947384.
KEGGiecj:JW2866.
eco:b2898.
PATRICi32121210. VBIEscCol129921_2993.

Organism-specific databases

EchoBASEiEB2549.
EcoGeneiEG12685. ygfZ.

Phylogenomic databases

eggNOGiENOG4106XY2. Bacteria.
COG0354. LUCA.
HOGENOMiHOG000261300.
InParanoidiP0ADE8.
KOiK06980.
OMAiGRMQSSF.
PhylomeDBiP0ADE8.

Enzyme and pathway databases

BioCyciEcoCyc:G7511-MONOMER.
ECOL316407:JW2866-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0ADE8.
PROiP0ADE8.

Family and domain databases

HAMAPiMF_01175. tRNA_modifying_YgfZ. 1 hit.
InterProiIPR006222. GCV_T_N.
IPR029043. GcvT/YgfZ_C.
IPR023758. tRNA-modifying_YgfZ.
IPR017703. YgfZ/GcvT_CS.
[Graphical view]
PfamiPF01571. GCV_T. 1 hit.
[Graphical view]
SUPFAMiSSF101790. SSF101790. 1 hit.
TIGRFAMsiTIGR03317. ygfZ_signature. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiYGFZ_ECOLI
AccessioniPrimary (citable) accession number: P0ADE8
Secondary accession number(s): P39179, Q2M9U3, Q46826
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 93 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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.