3MOJ,5B88


Conserved Protein Domain Family
RRM_DbpA

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cd12252: RRM_DbpA 
Click on image for an interactive view with Cn3D
RNA recognition motif (RRM) found in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases
This subfamily corresponds to the C-terminal RRM homology domain of dbpA proteins implicated in ribosome biogenesis. They bind with high affinity and specificity to RNA substrates containing hairpin 92 of 23S rRNA (HP92), which is part of the ribosomal A-site. The majority of dbpA proteins contain two N-terminal ATPase catalytic domains and a C-terminal RNA binding domain, an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain). The catalytic domains bind to nearby regions of RNA to stimulate ATP hydrolysis and disrupt RNA structures. The C-terminal domain is responsible for the high-affinity RNA binding. Several members of this family lack specificity for 23S rRNA. These proteins can generally be distinguished by a basic region that extends beyond the C-terminal domain.
Statistics
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PSSM-Id: 409698
Aligned: 59 rows
Threshold Bit Score: 42.1489
Created: 22-Dec-2011
Updated: 25-Oct-2021
Structure
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Program:
Drawing:
Aligned Rows:
 
RNA binding
Conserved site includes 18 residues -Click on image for an interactive view with Cn3D
Feature 1:RNA binding site [nucleic acid binding site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1            #    #### ### ##     #  ####                             ##  #  
3MOJ_B      2 KLYFNGGKkkKIRAVDFVGTIAKidGVSADDIGIITIMdNASYVEILngKGPHVLKVMKNttvkGKQLKVN 72  Bacillus subtilis
Q095H6    739 RLWVNLGKqdGLDDAGLTAALEGa-GAPAGKVARIDLRpTYAYVFVAdeDADAFEATHGKph-gEKTIKLE 807 Stigmatella aurantiaca DW4/3-1
Q095H6    644 KLWTNLGMddGLDEAKFTAALEAa-GAPAGKVLKVILRpTYGYAYVAeaDAPAFDVLSGKqh-gEKTLKVE 712 Stigmatella aurantiaca DW4/3-1
Q9S531    547 KLWVNLGTadGLGPGSIATALEDa-GAPVGKVVRAELRpTFAYVFVAe-EDAAAFETINGkqhgAKTLRVE 615 Myxococcus xanthus
Q26CN9    480 TYFINLGLkdDINKGALLGYVCDttGISGAQIGRIVMDkTHSYMDVAedVASQILTLDGKqr-nGHDLRVN 549 Flavobacteria bacterium BBFL7
Q64UR5    366 TIYIGKGKkdKLSKIDIAGFLYKkgNLAREDVGAIDVKdHYAFVAVRrpKMKQLLTLIRGekikGMKTVIE 436 Bacteroides fragilis
ADN75958  368 TLMVNAGRraRLRKGDLMGALIKaaGVPADAIVAIELMpDHSYVTLSkrYVATALAALDGgevkGKPVKVR 438 Ferrimonas balearica DSM 9799
P21693    384 TLCIDGGKkaKMRPGDVLGALTGdiGLDGADIGKIAVHpAHVYVAVRqaVAHKAWKQLQGgkikGKTCRVR 454 Escherichia coli H736
CBK63867  471 RLFLALGGrdGYTARRIVEMLKRkcGLRDKNIDDVRVFeNYSLVSVPfsDAEAVVGQLNAs--gGRRRIAK 539 Alistipes shahii WAL 8301
AEH07350  458 RLFIALGKkdGMNPRKLVEYIEDetGVRGRYIDDVAVFeNFSYITVSsrDADKIMKTLGRtr-rNGKSIVD 527 Methanothermococcus okinawe...

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