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Protein

Uncharacterized HTH-type transcriptional regulator YddM

Gene

yddM

Organism
Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi24 – 4320H-T-H motifPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciECOL199310:C1909-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Uncharacterized HTH-type transcriptional regulator YddM
Gene namesi
Name:yddM
Ordered Locus Names:c1909
OrganismiEscherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
Taxonomic identifieri199310 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000001410 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 9494Uncharacterized HTH-type transcriptional regulator YddMPRO_0000149760Add
BLAST

Proteomic databases

PRIDEiP67700.

Interactioni

Protein-protein interaction databases

STRINGi199310.c1909.

Structurei

Secondary structure

1
94
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi9 – 2012Combined sources
Helixi24 – 318Combined sources
Helixi35 – 428Combined sources
Helixi50 – 5910Combined sources
Helixi64 – 8017Combined sources
Helixi85 – 873Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2ICPX-ray1.88A1-94[»]
2ICTX-ray1.63A1-94[»]
ProteinModelPortaliP67700.
SMRiP67700. Positions 1-94.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP67700.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini13 – 6755HTH cro/C1-typePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the VapA/VapI family.Curated
Contains 1 HTH cro/C1-type DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG41084S7. Bacteria.
COG3093. LUCA.
HOGENOMiHOG000265974.
OMAiGRSAESW.
OrthoDBiEOG67DPQ2.

Family and domain databases

Gene3Di1.10.260.40. 1 hit.
InterProiIPR001387. Cro/C1-type_HTH.
IPR010982. Lambda_DNA-bd_dom.
IPR013430. Toxin_antidote_HigA.
[Graphical view]
PfamiPF01381. HTH_3. 1 hit.
[Graphical view]
SMARTiSM00530. HTH_XRE. 1 hit.
[Graphical view]
SUPFAMiSSF47413. SSF47413. 1 hit.
TIGRFAMsiTIGR02607. antidote_HigA. 1 hit.
PROSITEiPS50943. HTH_CROC1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P67700-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKMANHPRPG DIIQESLDEL NVSLREFARA MEIAPSTASR LLTGKAALTP
60 70 80 90
EMAIKLSVVI GSSPQMWLNL QNAWSLAEAE KTVDVSRLRR LVTQ
Length:94
Mass (Da):10,401
Last modified:October 11, 2004 - v1
Checksum:iE330280EDA2AEC1B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014075 Genomic DNA. Translation: AAN80368.1.
RefSeqiWP_000781370.1. NC_004431.1.

Genome annotation databases

EnsemblBacteriaiAAN80368; AAN80368; c1909.
KEGGiecc:c1909.
PATRICi18281717. VBIEscCol75197_1777.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014075 Genomic DNA. Translation: AAN80368.1.
RefSeqiWP_000781370.1. NC_004431.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2ICPX-ray1.88A1-94[»]
2ICTX-ray1.63A1-94[»]
ProteinModelPortaliP67700.
SMRiP67700. Positions 1-94.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi199310.c1909.

Proteomic databases

PRIDEiP67700.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN80368; AAN80368; c1909.
KEGGiecc:c1909.
PATRICi18281717. VBIEscCol75197_1777.

Phylogenomic databases

eggNOGiENOG41084S7. Bacteria.
COG3093. LUCA.
HOGENOMiHOG000265974.
OMAiGRSAESW.
OrthoDBiEOG67DPQ2.

Enzyme and pathway databases

BioCyciECOL199310:C1909-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP67700.

Family and domain databases

Gene3Di1.10.260.40. 1 hit.
InterProiIPR001387. Cro/C1-type_HTH.
IPR010982. Lambda_DNA-bd_dom.
IPR013430. Toxin_antidote_HigA.
[Graphical view]
PfamiPF01381. HTH_3. 1 hit.
[Graphical view]
SMARTiSM00530. HTH_XRE. 1 hit.
[Graphical view]
SUPFAMiSSF47413. SSF47413. 1 hit.
TIGRFAMsiTIGR02607. antidote_HigA. 1 hit.
PROSITEiPS50943. HTH_CROC1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CFT073 / ATCC 700928 / UPEC.
  2. "Crystal structures of Phd-Doc, HigA, and YeeU establish multiple evolutionary links between microbial growth-regulating toxin-antitoxin systems."
    Arbing M.A., Handelman S.K., Kuzin A.P., Verdon G., Wang C., Su M., Rothenbacher F.P., Abashidze M., Liu M., Hurley J.M., Xiao R., Acton T., Inouye M., Montelione G.T., Woychik N.A., Hunt J.F.
    Structure 18:996-1010(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.63 ANGSTROMS).

Entry informationi

Entry nameiYDDM_ECOL6
AccessioniPrimary (citable) accession number: P67700
Secondary accession number(s): P76125
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: October 11, 2004
Last modified: November 11, 2015
This is version 71 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

The crystal structure has erroneously been identified as HigA, the sequence submitted is in fact that of YddM.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.