InterPro : IPR004087

Name  K Homology domain Short Name  KH_dom
Type  Domain Description  The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. An evolutionarily conserved sequence of around 70 amino acids, the KH domain is present in a wide variety of nucleic acid-binding proteins. The KH domain binds RNA, and can function in RNA recognition []. It is found in multiple copies in several proteins, where they can function cooperatively or independently. For example, in the AU-rich element RNA-binding protein KSRP, which has 4 KH domains, KH domains 3 and 4 behave as independent binding modules to interact with different regions of the AU-rich RNA targets []. The solution structure of the first KH domain of FMR1 []and of the C-terminal KH domain of hnRNP K []determined by nuclear magnetic resonance(NMR) revealed a beta-alpha-alpha-beta-beta-alpha structure. Proteins containing KH domains include:Bacterial and organelle PNPases [].Archaeal and eukaryotic exosome subunits [].Eukaryotic and prokaryotic RS3 ribosomal proteins [].Vertebrate fragile X mental retardation protein 1 (FMR1) [].Vigilin, which has 14 KH domains [].AU-rich element RNA-binding protein KSRP.hnRNP K, which contains 3 KH domains.Human onconeural ventral antigen-1 (NOVA-1) [].According to structural analyses [, , ], the KH domain can be separated in two groups - type 1 and type 2.

Sequence Features

GO Displayer


InterPro protein domain ID --> Contigs



2 Child Features

Id Name Short Name Type
IPR004088 K Homology domain, type 1 KH_dom_type_1 Domain
IPR004044 K Homology domain, type 2 KH_dom_type_2 Domain

0 Contains

8 Found In

Id Name Short Name Type
IPR009019 K homology domain, prokaryotic type KH_prok-type Domain
IPR015946 K homology domain-like, alpha/beta KH_dom-like_a/b Domain
IPR005703 Ribosomal protein S3, eukaryotic/archaeal Ribosomal_S3_euk/arc Family
IPR005704 Ribosomal protein S3, bacterial Ribosomal_S3_bac Family
IPR012162 Polyribonucleotide nucleotidyltransferase PNPase Family
IPR019975 KH-domain/beta-lactamase-domain protein, archaea KH-dom/beta-lactamase-dom_arc Family
IPR017705 Ribonuclease Y Ribonuclease_Y Family
IPR019964 KH domain protein, archaea KH_domain_protein_archaea Family

0 Parent Features

10 Publications

First Author Title Year Journal Volume Pages
Musco G The solution structure of the first KH domain of FMR1, the protein responsible for the fragile X syndrome. 1997 Nat Struct Biol 4 712-6
Baber JL High precision solution structure of the C-terminal KH domain of heterogeneous nuclear ribonucleoprotein K, a c-myc transcription factor. 1999 J Mol Biol 289 949-62
Grishin NV KH domain: one motif, two folds. 2001 Nucleic Acids Res 29 638-43
Lewis HA Crystal structures of Nova-1 and Nova-2 K-homology RNA-binding domains. 1999 Structure 7 191-203
García-Mayoral MF The structure of the C-terminal KH domains of KSRP reveals a noncanonical motif important for mRNA degradation. 2007 Structure 15 485-98
Matus-Ortega ME The KH and S1 domains of Escherichia coli polynucleotide phosphorylase are necessary for autoregulation and growth at low temperature. 2007 Biochim Biophys Acta 1769 194-203
Oddone A Structural and biochemical characterization of the yeast exosome component Rrp40. 2007 EMBO Rep 8 63-9
Gloor BP [Transport of 131I-hippuric acid and 22Na from the space between retina and pigment epithelium after experimental amotio]. 1975 Mod Probl Ophthalmol 15 115-8
Darnell JC Kissing complex RNAs mediate interaction between the Fragile-X mental retardation protein KH2 domain and brain polyribosomes. 2005 Genes Dev 19 903-18
Kruse C The multi-KH protein vigilin associates with free and membrane-bound ribosomes. 2003 Cell Mol Life Sci 60 2219-27

To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)