5K0Y,1S1H,1VW9,2XZM,2ZKQ,3IZB,3J38,3J7A,3J80,3ZEY,4BSZ,4CUY,4KZX,4UER,5IT9,4UJF,5OPT,5XXU,5XYI,6AZ1,6P4G,6ZN5


Conserved Protein Domain Family
KH-II_40S_S3

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cd02413: KH-II_40S_S3 
type II K-homology (KH) RNA-binding domain found in 40S ribosomal protein S3 and similar proteins
40S ribosomal protein S3, also called small ribosomal subunit protein uS3, is part of the head region of the 40S ribosomal subunit and is involved in translation. It is believed to interact with mRNA as it threads its way from the latch into the channel. 40S ribosomal protein S3 has endonuclease activity and plays a role in repair of damaged DNA. It cleaves phosphodiester bonds of DNAs containing altered bases with broad specificity and cleaves supercoiled DNA more efficiently than relaxed DNA. Members of this family are mainly from prokaryotes and contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid).
Statistics
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PSSM-Id: 411784
Aligned: 75 rows
Threshold Bit Score: 111.844
Created: 18-Feb-2005
Updated: 25-Oct-2021
Structure
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Program:
Drawing:
Aligned Rows:
 
RNA bindingGXXG motif
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
Feature 1:RNA binding site [nucleic acid binding site]
Evidence:
  • Structure:5K0Y; Oryctolagus cuniculus ribosomal protein uS3 interacts with rRNA (18S ribosomal RNA) and mRNA, contacts at 4A

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1        #####          #      #                         ####                            
5K0Y_GG        5 ISKKRKFVaDGIFKAELNEFLTRELaEDGYSGVEVRVTPtRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFpeGSV 84  rabbit
2XZM_C         8 INKKKKFVaDGVFNAELHSFFSKSLqDAGYAGIEVRRTPtKTEIRIKATKPQQVIGVEGKKHKELTQFLQKRFGYsdDQI 87  Tetrahymena the...
5OPT_MM        4 LSKKRMIIrDGVFYAELFEFLKRELaDDGFAGVEHRVTStRTEIVIRATKTREVLGEKGRRIRELTACLQQRFHYkeGKL 83  Trypanosoma cru...
5XYI_D         6 CTKVRRIIeTGLFYAELNELLTRELtKEGYGGCEVRQTPtRTEIIIKAANTKEFVDNHGRRLQEVRMMIQKRWRLkeDSL 85  Trichomonas vag...
6AZ1_C         4 LSKKRMIIrDGVFYAELFEFLKRELaEEGFSGVSYHVTTlRTEIVIKATKTREVLGVNGRRIRELTACIQQRFNYkeGKL 83  Leishmania dono...
AAK39747       6 LSLKKKFVaDGVVYSEINEFLERELkENGFSGIKIKKKIeKVEIIIKSSKAHTIIGFKGKRIRELNVLLKKRFNFgeNKL 85  Guillardia theta
XP_001708724  11 NVYYSKYLnDCIMEAELHEFFSRELvDAGYASCSLCRTIdSICVIIQCAEPEVVMGDNHYRLHKIEYLLAGRFMCdpKNF 90  Giardia lamblia...
Q8SQM3         4 DQVLERFMkNGLMNAELKEFFEKALvNEGFSTMELRMQEtPIKIILKVAKPHEAIGEKKFRLRQFQHLAAQRLEVpdESV 83  Encephalitozoon...
KII72969       5 ISKKRLFVkNGLLYSELNSFFKQQLmDDGYVGLEIRPRGtNTDLILMVIRPSDVVGDKGRRIRELQTLVQRKFNYdpDKI 84  Thelohanellus k...
KNH01398       4 LNKKKKFVaDGVFAAELNEFLKRQLaEFGYCGVEHRVTPqRTDIFIRATRTQDVMGPKNERLRQLTTLIQRRFNFpeGGL 83  Perkinsela sp. ...
Feature 1             #   # 
5K0Y_GG       85 ELYAEKVATRG 95  rabbit
2XZM_C        88 QIWAEPIKFKG 98  Tetrahymena thermophila
5OPT_MM       84 QLFAERVEVRG 94  Trypanosoma cruzi strain CL Brener
5XYI_D        86 EIFIDRIQRKG 96  Trichomonas vaginalis
6AZ1_C        84 QLYVERVEVRG 94  Leishmania donovani
AAK39747      86 VLYVEKINNRN 96  Guillardia theta
XP_001708724  91 NIWVDKIIKRG 101 Giardia lamblia ATCC 50803
Q8SQM3        84 EIVVEKVHEKG 94  Encephalitozoon cuniculi GB-M1
KII72969      85 RIFVDPVRSRG 95  Thelohanellus kitauei
KNH01398      84 QIYTDKVLRKG 94  Perkinsela sp. CCAP 1560/4

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