K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6324119  188 VTLEIKLNKTQITFLIGAKGTRIESLREKSGASIKIIPISDkmtahernhpeSVQQTILISGDLYSIALAVTSIES 263
Cdd:cd22458   1 VTWEIKLPQALCGRLIGAKGKNIKALSEKSGASIRLIPISN-----------SSQQTIHLSGTDKQIALAISSIEE 65

type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic recombination 1 protein (MER1) and similar proteins; MER1 is required for chromosome pairing and genetic recombination. It may function to bring the axial elements of the synaptonemal complex corresponding to homologous chromosomes together by initiating recombination. MER1 might be responsible for regulating the MER2 gene and/or gene product.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6324119  188 VTLEIKLNKTQITFLIGAKGTRIESLREKSGASIKIIPISDkmtahernhpeSVQQTILISGDLYSIALAVTSIES 263
Cdd:cd22458   1 VTWEIKLPQALCGRLIGAKGKNIKALSEKSGASIRLIPISN-----------SSQQTIHLSGTDKQIALAISSIEE 65

K homology RNA-binding domain;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6324119     188 VTLEIKLNKTQITFLIGAKGTRIESLREKSGASIKIIPisdkmtahernhPESVQQTILISGDLYSIALAVTSIESAL 265
Cdd:smart00322   3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG------------PGSEERVVEITGPPENVEKAAELILEIL 68

type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic recombination 1 protein (MER1) and similar proteins; MER1 is required for chromosome pairing and genetic recombination. It may function to bring the axial elements of the synaptonemal complex corresponding to homologous chromosomes together by initiating recombination. MER1 might be responsible for regulating the MER2 gene and/or gene product.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6324119  188 VTLEIKLNKTQITFLIGAKGTRIESLREKSGASIKIIPISDkmtahernhpeSVQQTILISGDLYSIALAVTSIES 263
Cdd:cd22458   1 VTWEIKLPQALCGRLIGAKGKNIKALSEKSGASIRLIPISN-----------SSQQTIHLSGTDKQIALAISSIEE 65

second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the second one.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6324119  199 ITFLIGAKGTRIESLREKSGASIKIIPISDKMTAHERNHPESVQQTilISGDLYSIALAVTSIES 263
Cdd:cd22447  15 RARIIGKKGANLKQIREKTGVRIDIPPRDADAAPADEDDDTMVEVT--ITGDEFNVQHAKQRIEE 77

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6324119  190 LEIKLNKTQITFLIGAKGTRIESLREKSGASIKIipisdkmtahERNHPESVQQTILISGDLYSIALAVTSIE 262
Cdd:cd00105   1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQI----------PKEGEGSGERVVTITGTPEAVEKAKELIE 63

first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6324119  188 VTLEIKLNKTQITFLIGAKGTRIESLREKSGASIKIIPISDKMTAHERNHPESVqqTILISGDLYSIALAVTSIE 262
Cdd:cd22446   7 VTITISVPSSVRGAIIGSRGKNLKSIQDKTGTKIQIPKRNEEGNYDEDDDDETV--EISIEGDAEGVELAKKEIE 79

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6324119  196 KTQITFLIGAKGTRIESLREKSGASIKIIP---------ISDKMtahernhpesVQqtilISGDLYSIALAVTSIESAL 265
Cdd:cd22460   8 SSQAGSLIGKGGAIIKQIREESGASVRILPeeelppcasPDDRV----------VQ----ISGEAQAVKKALELVSSRL 72

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6324119  188 VTLEIKLNKTQITFLIGAKGTRIESLREKSGASIKIipISDKMtahernhPESVQQTILISGDLYSIALAVTSI 261
Cdd:cd22520   2 VTLRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQV--AGDLL-------PNSTERAVTVSGVPDAIIQCVRQI 66

third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324119  189 TLEIKLNKTQITFLIGAKGTRIESLREKSGASIKIIpisdkmtaherNHPE-SVQQTILISGDLYSIALA 257
Cdd:cd22439   3 TQEITIPNDLIGCIIGKGGTKINEIRQLSGATIKIA-----------NSEDgSTERSVTITGTPEAVSLA 61

third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6324119  197 TQITF-------LIGAKGTRIESLREKSGASIKIipisdkmtahERNHPESVQQTILISGDLYSIALA 257
Cdd:cd22434   4 TQVTIpkdlagsIIGKGGQRIRQIRHESGASIKI----------DEPLPGSEDRIITITGTQDQIQNA 61

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6324119  187 IVTLEIKLNKTQITFLIGAKGTRIESLREKSGASIKIIPisdkmtahernhPESVQQTILISGDLYSIALAVTSIES 263
Cdd:cd02394   1 MAFTTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPD------------DEANSDEIRIEGSPEGVKKAKAEILE 65