Conserved Protein Domain Family
RRM_EcDbpA_like

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cd12501: RRM_EcDbpA_like 
RNA recognition motif (RRM) found in Escherichia coli RNA helicase dbpA and similar proteins
This subgroup corresponds to the C-terminal RRM homology domain of dbpA. E. coli dbpA is a member of the DbpA subfamily of prokaryotic DEAD-box rRNA helicases that have been implicated in ribosome biogenesis. It binds with high affinity and specificity for RNA substrates containing hairpin 92 of 23S rRNA (HP92) with either 3' or 5' extensions. As a non-processive ATP-dependent helicase, DbpA destabilizes and unwinds short <9bp (base pairs) RNA duplexes as well as long duplex RNA stretches. It disrupts RNA helices exclusively in a 3'- 5' direction and requires a single-stranded loading site 3' of the substrate helix. dbpA contains 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 binds specifically to hairpin 92.
Statistics
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PSSM-Id: 409924
Aligned: 13 rows
Threshold Bit Score: 120.037
Created: 5-Mar-2012
Updated: 25-Oct-2021
Structure
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Aligned Rows:
 
putative RNA
Feature 1:putative RNA binding site [nucleic acid binding site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1               #    #### ### ##      #  ####                             ##  #    
P21693       384 TLCIDGGKKAKMRPGDVLGALTGd-iGLDGADIGKIAVHPAHVYVAVRqaVAHKAWKQLQGGKIKGKTCRVRLL 456 Escherichia coli H736
Q5WUX7       395 TLCIASGKKDKIRPGDILGALTKd-aGLAGNTIGKINITAMYSYVAIHrsQADKAYQYLQSGKLKGRKVNVRKI 467 Legionella pneumophil...
Q6MN67       431 TISISGGRKDKLRPGDILGALTGaagGLTSADVGKIEIQDKISFVAVSakVADGAMQKLRDGRIKGQKFQVKFV 504 Bdellovibrio bacterio...
Q31H30       394 TLLIDGGKKNKLRPGDILGALTAn-dVLNAGQVGKIKITDKKSYVAVTrsMFKQALKQLGAGKLKGRNFRVHKL 466 Thiomicrospira crunog...
Q1ZEY3       388 TLRIEGGKKQKIRPGDIVGALTGd-dGISGDDIGKIQISPNWAYVAVQrqCIKTAFKKLSTGKLKGRKYRVMVV 460 Psychromonas sp. CNPT3
Q07Y62       395 TIQIEAGKKQKIRPGDIVGALTGg-nGLDFNDIGKIKVTDFRAYFAVKsnVSKQAMNIISKGKLKGRSYRAWFM 467 Shewanella frigidimar...
Q485I3       394 TIQIDGGKKQKVRAGDILGALTGd-nGVQGSQVGKISVLDNKAYVAVTkaALNLALKKISKGKMKGRTFNARHL 466 Colwellia psychreryth...
Q21N20       391 TLQIDGGKKQKVRPGDIVGGLTGe-nGIAGTEIGKISVFDNSSYVAVAlpVMKTALNKIRDGKLKGRNFRVRAI 463 Saccharophagus degrad...
Q8D7L6       360 TIQILGGKKQKVRAGDILGSLTKe-aGIDGKLIGKINILPMVSYVAIDnsVAKIAEQQLQNGKMKGRNFKARIM 432 Vibrio vulnificus
XP_001617631 188 TIHINASRKDKIRPGDVLGALTAd-lGYTREQVGKIDINEFATYVAVDrkIAHDVVARLNSGKIKGRTVKARLL 260 starlet sea anemone
Q15YC1       386 TLCVDGGKKAKLRPGDLLGALTKe-aEIPGDDIGKIHITEFHAYVAVKtrSVKRAMRQLGEGKIKGKKFKVRKF 458 Pseudoalteromonas atl...
Q1ZTU1       388 TLMIDGGKKQKVRPGDILGALTGe-nGIAGSDVGKINVFDFCAYVAVKreVARAALKKLENGRIKGRNFRSRQL 460 Photobacterium angust...
AEP35861     360 TISIKGGKKDKLRKADIIGAMTQh-lQIPFEEIGKIHVADFVSFVAVRrdQAEDILLRLREIPIKNRSWMMRLM 432 Taylorella asinigenit...

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