 |
InterPro: IPR003583 Helix-hairpin-helix DNA-binding motif, class 1
Protein matches
|
UniProtKB Matches: 15766 proteins |
|
|
Accession
|
IPR003583 Hlx-hairpin-Hlx_DNA-bd_motif |
|
Type
|
Conserved_site |
|
Signatures
|
|
|
InterPro Relationships
|
|
Children
|
IPR000445 Helix-hairpin-helix motif
|
|
Found in
|
IPR000085 Bacterial DNA recombination protein RuvA
IPR000093 RecR protein
IPR001679 NAD-dependent DNA ligase
IPR002008 DNA-directed DNA polymerase, family X, beta-like
IPR002054 DNA-directed DNA polymerase, family X
IPR003265 HhH-GPD domain
IPR004509 Competence protein ComEA, helix-hairpin-helix region
IPR004787 Competence protein ComEA
IPR004791 Excinuclease ABC, C subunit
IPR005759 Endonuclease III/Nth
IPR005760 A/G-specific adenine glycosylase MutY, bacterial form
IPR006345 DNA helicase, RecD/TraA type
IPR010994 RuvA domain 2-like
IPR010995 DNA repair Rad51/transcription factor NusA, alpha-helical
IPR010996 DNA-directed DNA polymerase, family X, beta-like, N-terminal
IPR011257 DNA glycosylase
IPR011938 DNA recombination and repair protein RadA
IPR011940 Meiotic recombinase Dmc1
IPR011941 DNA recombination and repair protein Rad51
IPR012401 DNA mismatch repair protein, archaeal
IPR016467 DNA recombination and repair protein, RecA-like
IPR016960 Uncharacterised conserved protein UCP030823, kinase, HhH DNA-binding
IPR018320 DNA polymerase 1
IPR020047 5'-3' exonuclease, SAM-fold domain
|
|
GO Term annotation
|
|
Process
|
GO:0006281 DNA repair
|
|
Function
|
GO:0003677 DNA binding
|
|
InterPro annotation
|
|
 Entry Details in BioMart
|
|
Abstract
|
The HhH motif is an around 20 amino acids domain present in prokaryotic and
eukaryotic non-sequence-specific DNA binding proteins [1, 2, 3].
The HhH motif is similar to, but distinct from, the HtH motif. Both of these
motifs have two helices connected by a short turn. In the HtH motif the second
helix binds to DNA with the helix in the major groove. This allow the contact
between specific base and residues throughout the protein. In the HhH motif
the second helix does not protrude from the surface of the protein and
therefore cannot lie in the major groove of the DNA. Crystallographic studies
suggest that the interaction of the HhH domain with DNA is mediated by amino
acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal
end of the second helix [1]. This interaction could involve the formation of
hydrogen bonds between protein backbone nitrogens and DNA phosphate groups
[4].
The structural difference between the HtH and HhH domains is reflected at the
functional level: whereas the HtH domain, found primarily in gene regulatory
proteins, binds DNA in a sequence specific manner, the HhH domain is rather
found in proteins involved in enzymatic activities and binds DNA with no
sequence specificity [4].
|
|
Structural links
|
SCOP:
a.60.12.1
,
a.60.2.1
,
a.60.2.2
,
a.60.2.3
,
a.60.2.4
,
a.60.2.5
,
a.60.2.6
,
a.60.2.7
,
a.60.3.1
,
a.60.4.1
,
a.60.4.2
,
a.60.6.1
,
a.60.7.1
,
a.96.1.1
,
a.96.1.2
,
c.9.2.1
,
e.49.1.1
,
i.1.1.2
,
i.8.1.1
|
|
Database links
|
|
|
Example proteins
|
P06746 DNA polymerase beta
P07903 DNA excision repair protein ERCC-1
P18105 Kinesin-like protein Nod
P25454 DNA repair protein RAD51
P94102 DNA repair protein RAD51 homolog 1
More proteins
Example Proteins Key
| InterPro entry accession number/name and structure databases |
Colour code |
| IPR003583 |
Helix-hairpin-helix DNA-binding motif, class 1 |
 |
| IPR002008 |
DNA-directed DNA polymerase, family X, beta-like |
 |
| IPR002054 |
DNA-directed DNA polymerase, family X |
 |
| IPR019843 |
DNA polymerase family X, binding site |
 |
| IPR010995 |
DNA repair Rad51/transcription factor NusA, alpha-helical |
 |
| IPR010994 |
RuvA domain 2-like |
 |
| IPR016467 |
DNA recombination and repair protein, RecA-like |
 |
| IPR010996 |
DNA-directed DNA polymerase, family X, beta-like, N-terminal |
 |
| IPR020587 |
DNA recombination/repair protein RecA, monomer-monomer interface |
 |
| IPR003593 |
ATPase, AAA+ type, core |
 |
| IPR020588 |
DNA recombination/repair protein RecA/RadB, ATP-binding domain |
 |
| IPR001752 |
Kinesin, motor domain |
 |
| IPR004579 |
DNA repair protein rad10 |
 |
| IPR013632 |
DNA recombination and repair protein Rad51, C-terminal |
 |
| IPR018944 |
DNA polymerase lambda, fingers domain |
 |
| IPR011941 |
DNA recombination and repair protein Rad51 |
 |
| IPR019821 |
Kinesin, motor region, conserved site |
 |
| IPR000445 |
Helix-hairpin-helix motif |
 |
|
PDB Chain |
 |
|
ModBase |
 |
|
CATH Domain |
 |
|
SWISS-MODEL |
 |
|
SCOP Domain |
 |
|
|
Additional Reading
|
|
Ippolito JA, Kanyo ZF, Wang D, Franceschi FJ, Moore PB, Steitz TA, Duffy EM.
Crystal structure of the oxazolidinone antibiotic linezolid bound to the 50S ribosomal subunit.
J. Med. Chem. 51 2008 3353-6
[PubMed: 18494460]
http://dx.doi.org/10.1021/jm800379d
|
|
|
Bebenek K, Garcia-Diaz M, Foley MC, Pedersen LC, Schlick T, Kunkel TA.
Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda.
EMBO Rep. 9 2008 459-64
[PubMed: 18369368]
http://dx.doi.org/10.1038/embor.2008.33
|
|
|
Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH.
Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation.
Mol. Cell 30 2008 315-24
[PubMed: 18471977]
http://dx.doi.org/10.1016/j.molcel.2008.02.025
|
|
|
Simonovic M, Steitz TA.
Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA.
RNA 14 2008 2372-8
[PubMed: 18818369]
http://dx.doi.org/10.1261/rna.1118908
|
|
|
Tang KH, Niebuhr M, Tung CS, Chan HC, Chou CC, Tsai MD.
Mismatched dNTP incorporation by DNA polymerase beta does not proceed via globally different conformational pathways.
Nucleic Acids Res. 36 2008 2948-57
[PubMed: 18385153]
http://dx.doi.org/10.1093/nar/gkn138
|
|
