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Conserved domains on  [gi|1776600706|gb|KAE8736507|]
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hypothetical protein F3Y22_tig00000002pilonHSYRG00371 [Hibiscus syriacus]

Protein Classification

RNA-binding protein( domain architecture ID 106745)

RNA-binding protein containing an RNA recognition motif (RRM)

CATH:  3.30.70.330
Gene Ontology:  GO:0003723
PubMed:  15853797
SCOP:  3000110

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 37-110 7.61e-27

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


The actual alignment was detected with superfamily member cd12420:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 76  Bit Score: 94.32  E-value: 7.61e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1776600706  37 RTIFIMFMHEDVKERELQNLLRWLPGFEASQVSYKGE--KPKGFALFSNAEFAVAAKDAFQKMVFDAKLKSFLHIE 110
Cdd:cd12420     1 RTLFVSGLPLDVKERELYNLFRPLPGYEASQLKFTGKntQPVGFVTFESRAAAEAAKDALQGMRFDPDTPQVLRLE 76
 
Name Accession Description Interval E-value
RRM_RBPMS_like cd12420
RNA recognition motif (RRM) found in RNA-binding protein with multiple splicing (RBP-MS)-like ...
 37-110 7.61e-27

RNA recognition motif (RRM) found in RNA-binding protein with multiple splicing (RBP-MS)-like proteins; This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4.


Pssm-ID: 409854 [Multi-domain]  Cd Length: 76  Bit Score: 94.32  E-value: 7.61e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1776600706  37 RTIFIMFMHEDVKERELQNLLRWLPGFEASQVSYKGE--KPKGFALFSNAEFAVAAKDAFQKMVFDAKLKSFLHIE 110
Cdd:cd12420     1 RTLFVSGLPLDVKERELYNLFRPLPGYEASQLKFTGKntQPVGFVTFESRAAAEAAKDALQGMRFDPDTPQVLRLE 76
 
Name Accession Description Interval E-value
RRM_RBPMS_like cd12420
RNA recognition motif (RRM) found in RNA-binding protein with multiple splicing (RBP-MS)-like ...
 37-110 7.61e-27

RNA recognition motif (RRM) found in RNA-binding protein with multiple splicing (RBP-MS)-like proteins; This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4.


Pssm-ID: 409854 [Multi-domain]  Cd Length: 76  Bit Score: 94.32  E-value: 7.61e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1776600706  37 RTIFIMFMHEDVKERELQNLLRWLPGFEASQVSYKGE--KPKGFALFSNAEFAVAAKDAFQKMVFDAKLKSFLHIE 110
Cdd:cd12420     1 RTLFVSGLPLDVKERELYNLFRPLPGYEASQLKFTGKntQPVGFVTFESRAAAEAAKDALQGMRFDPDTPQVLRLE 76
RRM_RBPMS cd12682
RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing ...
 36-110 1.16e-09

RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing (RBP-MS); This subfamily corresponds to the RRM of RBP-MS, also termed heart and RRM expressed sequence (hermes), an RNA-binding proteins found in various vertebrate species. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RBP-MS physically interacts with Smad2, Smad3 and Smad4 and plays a role in regulation of Smad-mediated transcriptional activity. In addition, RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development.


Pssm-ID: 410083 [Multi-domain]  Cd Length: 76  Bit Score: 50.81  E-value: 1.16e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1776600706  36 VRTIFIMFMHEDVKERELQNLLRWLPGFEASQVSYKGEKPKGFALFSNAEFAVAAKDAFQKMVFDAKLKSFLHIE 110
Cdd:cd12682     1 VRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDPEIPQTLRLE 75
RRM_RBPMS2 cd12683
RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing 2 ...
 36-110 9.13e-09

RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing 2 (RBP-MS2); This subfamily corresponds to the RRM of RBP-MS2, encoded by RBPMS2 gene, a paralog of RNA-binding protein with multiple splicing (RBP-MS). The biological function of RBP-MS2 remains unclear. Like RBP-MS, RBP-MS2 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410084 [Multi-domain]  Cd Length: 76  Bit Score: 48.50  E-value: 9.13e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1776600706  36 VRTIFIMFMHEDVKERELQNLLRWLPGFEASQVSYKGEKPKGFALFSNAEFAVAAKDAFQKMVFDAKLKSFLHIE 110
Cdd:cd12683     1 VRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVTFDSRAGAEAAKNALNGIRFDPENPQTLRLE 75
RRM_cpo cd12684
RNA recognition motif (RRM) found in Drosophila couch potato (cpo) coding RNA-binding protein ...
 36-110 2.28e-08

RNA recognition motif (RRM) found in Drosophila couch potato (cpo) coding RNA-binding protein and similar proteins; This subfamily corresponds to the RRM of Cpo, an RNA-binding protein encoded by Drosophila couch potato (cpo) gene. Cpo contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It may control the processing of RNA molecules required for the proper functioning of the peripheral nervous system (PNS).


Pssm-ID: 410085 [Multi-domain]  Cd Length: 83  Bit Score: 47.60  E-value: 2.28e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776600706  36 VRTIFIMFMHEDVKERELQNLLRWLPGFEASQVSY-----KGEKPKGFALFSNAEFAVAAKDAFQKMVFDAKLKSFLHIE 110
Cdd:cd12684     1 VRTLFVSGLPMDAKPRELYLLFRAYKGYEGSLLKVtskngKTTSPVGFVTFLSRQAAEAAKQDLQGVRFDPDLPQTLRLE 80
RRM_AtNSRA_like cd21618
RNA recognition motif (RRM) found in Arabidopsis thaliana nuclear speckle RNA-binding protein ...
 34-110 2.06e-06

RNA recognition motif (RRM) found in Arabidopsis thaliana nuclear speckle RNA-binding protein A (AtNSRA) and similar protein; AtNSRA is an alternative splicing (AS) regulator that binds to specific mRNAs and modulates auxin effects on the transcriptome. It can be displaced from its targets upon binding to AS competitor long non-coding RNA (ASCO-RNA). Members in this family contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410197 [Multi-domain]  Cd Length: 87  Bit Score: 42.25  E-value: 2.06e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1776600706  34 DEVRTIFIMFMHEDVKERELQNLLRWLPGFEASQV----SYKGEK-PKGFALFSNAEFAVAAKDAFQKMVFDAKLKS--F 106
Cdd:cd21618     1 DASSTLYVEGLPLDATEREVAHIFRPFPGFKSVRLvpkeGKRGRKlVLCFVDFADAQQAAAALETLQGYRLDEDDSDskG 80


                  ....
gi 1776600706 107 LHIE 110
Cdd:cd21618    81 LRIS 84
RRM_scw1_like cd12245
RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar ...
 38-110 8.25e-04

RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar proteins; This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins.


Pssm-ID: 409691 [Multi-domain]  Cd Length: 79  Bit Score: 35.29  E-value: 8.25e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1776600706  38 TIFIMFMHEDVKERELQNLLRWLPGFEASQVSYKGEKPKGFALFSNAEFAVAAKDAFQKMVFDAKLKSFLHIE 110
Cdd:cd12245     4 TLFVANLGPNVSEQELRQLFSRQPGFRRLRMHNKGGGPVCFVEFEDVPFATQALNHLQGAILSSSDRGGIRIE 76
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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