Protein Domain : IPR003583

Type:  Domain Name:  Helix-hairpin-helix DNA-binding motif, class 1
Description:  The HhH motif is a stretch of approximately 20 amino acids that is present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. 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 secondhelix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motifthe second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studiessuggest 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-terminalend of the second helix []. This interaction could involve the formation ofhydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatoryproteins and binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with nosequence specificity []. Short Name:  Hlx-hairpin-Hlx_DNA-bd_motif
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0 Child Features

0 Contains

1 Cross References

Identifier
SM00278

23 Found Ins

DB identifier Type Name
IPR002008 Family DNA polymerase family X, beta-like
IPR002054 Domain DNA-directed DNA polymerase X
IPR010996 Domain DNA polymerase beta-like, N-terminal domain
IPR005759 Family Endonuclease III
IPR011257 Domain DNA glycosylase
IPR003265 Domain HhH-GPD domain
IPR010994 Domain RuvA domain 2-like
IPR016467 Family DNA recombination and repair protein, RecA-like
IPR010995 Domain DNA repair Rad51/transcription factor NusA, alpha-helical
IPR011940 Family Meiotic recombinase Dmc1
IPR001679 Family NAD-dependent DNA ligase
IPR005760 Family A/G-specific adenine glycosylase MutY
IPR006345 Family DNA helicase, RecD-like
IPR000085 Family Bacterial DNA recombination protein RuvA
IPR018320 Family DNA polymerase 1
IPR004509 Domain Competence protein ComEA, helix-hairpin-helix domain
IPR022311 Family Uncharacterised conserved protein UCP005047, YshC
IPR004787 Family Competence protein ComEA
IPR011938 Family DNA recombination/repair protein RadA
IPR004791 Family UvrABC system, subunit C
IPR016960 Family Uncharacterised conserved protein UCP030823, kinase, HhH DNA-binding
IPR000093 Family DNA recombination protein RecR
IPR012401 Family DNA-binding protein MutS2, archaea

2 GO Annotations

GO Term Gene Name
GO:0003677 IPR003583
GO:0006281 IPR003583

2 Ontology Annotations

GO Term Gene Name
GO:0003677 IPR003583
GO:0006281 IPR003583

0 Parent Features

124 Proteins

DB identifier UniProt Accession Secondary Identifier Organism Name Length
33407.m000028 B9TJD0 PAC:16825818 Ricinus communis 171  
38551 A4RY29 PAC:27416533 Ostreococcus lucimarinus 794  
Traes_3B_3774EFFE7.1 W5CT03 PAC:31752313 Triticum aestivum 436  
Traes_3B_3774EFFE7.2 PAC:31752314 Triticum aestivum 429  
Traes_3DS_FA579628B.2 PAC:32010579 Triticum aestivum 396  
Traes_3DS_FA579628B.1 PAC:32010578 Triticum aestivum 402  
Pahal.E00166.1 A0A2S3HN56 PAC:32499481 Panicum hallii 459  
Sphfalx0033s0069.1.p PAC:32626125 Sphagnum fallax 1119  
Sevir.5G456500.1.p A0A4U6UU96 PAC:32673322 Setaria viridis 452  
Seita.5G450100.1.p A0A368RG39 PAC:32684854 Setaria italica 452  
Bradi2g10500.1.p I1HEH0 PAC:32771498 Brachypodium distachyon 570  
Pp3c23_20740V3.1.p A0A2K1IK62 PAC:32948613 Physcomitrium patens 1051  
Pp3c23_20740V3.2.p A0A2K1IK62 PAC:32948614 Physcomitrium patens 1051  
Pp3s32_280V3.1.p PAC:32948403 Physcomitrium patens 2359  
Pp3s356_30V3.1.p PAC:32937655 Physcomitrium patens 673  
Zosma282g00050.1 A0A0K9PD57 PAC:33170561 Zostera marina 555  
Brdisv1Per11015058m.p PAC:33214793 Brachypodium distachyon Per1 570  
Brdisv1Uni21014158m.p I1HEH0 PAC:33281136 Brachypodium distachyon Uni2 570  
Brdisv1Bd3-1_r1011562m.p PAC:33314694 Brachypodium distachyon Bd3-1 570  
Brdisv1BdTR7a1014944m.p PAC:33363082 Brachypodium distachyon BdTR7a 570  
Brdisv1Koz-11014998m.p PAC:33410341 Brachypodium distachyon Koz-1 570  
Brdisv20Bd21Ref1015872m.p I1HEH0 PAC:33429800 Brachypodium distachyon Bd21 AnntCtrl 570  
Brdisv1ABR9_r1014397m.p PAC:33535828 Brachypodium distachyon ABR9 457  
Brdisv1BdTR13a1015674m.p I1HEH0 PAC:33583991 Brachypodium distachyon BdTR13a 570  
Brdisv1pangenome1029141m.p I1HEH0 PAC:33608789 Brachypodium distachyon Pangenome 570  
Brdisv1ABR6_r1015071m.p I1HEH0 PAC:33687030 Brachypodium distachyon ABR6 570  
Brdisv1ABR21014903m.p I1HEH0 PAC:33715211 Brachypodium distachyon ABR2 570  
Brdisv1Bis-11014256m.p I1HEH0 PAC:33759199 Brachypodium distachyon Bis-1 570  
Brdisv1S8iiC1014665m.p I1HEH0 PAC:33863558 Brachypodium distachyon S8iic 570  
Brdisv1Tek-21013810m.p PAC:33894681 Brachypodium distachyon Tek-2 570  

4 Publications

First Author Title Year Journal Volume Pages PubMed ID
            8692686
            9973609
            7664751
            9987128