1MMS,2FTC,1VS6,1NKW,1S72,1YL3,1OLN,2ZKR


Conserved Protein Domain Family
Ribosomal_L11

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cd00349: Ribosomal_L11 
Click on image for an interactive view with Cn3D
Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal protein L12, which is distinct from the L12 involved in the formation of the L7/L12 stalk. The C-terminal domain (CTD) of L11 is essential for binding 23S rRNA, while the N-terminal domain (NTD) contains the binding site for the antibiotics thiostrepton and micrococcin. L11 and 23S rRNA form an essential part of the GTPase-associated region (GAR). Based on differences in the relative positions of the L11 NTD and CTD during the translational cycle, L11 is proposed to play a significant role in the binding of initiation factors, elongation factors, and release factors to the ribosome. Several factors, including the class I release factors RF1 and RF2, are known to interact directly with L11. In eukaryotes, L11 has been implicated in regulating the levels of ubiquinated p53 and MDM2 in the MDM2-p53 feedback loop, which is responsible for apoptosis in response to DNA damage. In bacteria, the "stringent response" to harsh conditions allows bacteria to survive, and ribosomes that lack L11 are deficient in stringent factor stimulation.
Statistics
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PSSM-Id: 100101
View PSSM: cd00349
Aligned: 137 rows
Threshold Bit Score: 109.848
Threshold Setting Gi: 11466196
Created: 6-Mar-2002
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 19 residues -Click on image for an interactive view with Cn3D
Feature 1:23S rRNA interface [nucleic acid binding site]
Evidence:
  • Structure:1MMS_A; Thermotoga maritima ribosomal protein L11 binds 23S rRNA (1MMS_C), defined using 3.5 A contacts
    View structure with Cn3D
  • Structure:1VS6_I; E. coli ribosomal protein L11 binds 23S rRNA (1VS6_B), defined using 3.5 A contacts
    View structure with Cn3D
  • Structure:1NKW_G; Deinococcus radiodurans ribosomal protein L11 binds 23S rRNA (1NKW_0), defined using 4.5 A contacts
    View structure with Cn3D
  • Comment:The structure 1NKW lacks side chain atoms, so 4.5 A contacts were used in place of 3.5 A contacts

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1         #                   #                                                ###   #   
1MMS_A         8 IKLQLPAGKATPappvGPALGQh--GVNIM-EFCKRFNAETADk-AGMILPVVITVYEd-kSFTFIIktPPASFLLKKA- 81
gi 67464170   13 LVVKVVAGDAAAgaslGPKVGPl--GLNPK-KTGDDLAKSTLAw-KGLRVTVRITVVNr--VATYEVi-PSAAALILKAl 85
gi 121916871   8 IKCRVWGGETGVtsklAPKLGPl--GVPAP-KVAQEVAKATEKf-KGFRATVKITVQNr--EFKVDVe-NSTSTLLIAAl 80
gi 3914677     6 IKIMVEGGNVKPgpplAPTLSQl--GLNVG-EVVKKLNEATSSf-KGMSVPVTIEVDSstkKYEIKVgiPTTTALLLKE- 80
gi 18313825    6 VTVPLQGGKVAVnpqfQDALKQi--GLDPN-AVVQRVQEELKKvgKYPVQKVEVEVVSp-sKYEVKIylPPIGDLLLKL- 80
gi 126465989   6 IKVMVEGGKANPgpplGPTLSPl--RVNVM-EVVKAINEATKDf-EGLTVPVEIIVDTstrKFEVKVgiPTTTALLLKE- 80
gi 124028449   6 INVKVRGGEAKPapplAPAIEKl--GLDVN-KVVEDINKATEKy-KGFEVAVKLIVDEntkEYEIEVkpPTTTELLLKA- 80
gi 156937968   6 LTFSVEGGNAKPappiKPALESv--GLDPN-EVVQKINEVTKRy-KGFTVTVKVIVDPdtkEYEIEVepPNITELLLKL- 80
gi 145476333  13 INIKVFGGEGGPastlAPKLGPl--GLNPK-QVGDKIIAESGKw-KGIRVMVNLRCQNr--NADVTVi-PTSSALLIKEi 85
gi 160948256  13 VFIKCRGGDILPeyllAPKFFGfdfRWNEIkFIAKEISDITRDy-KDLKVTIQFTVQNr--KAEMMVv-PTASSLIIKAl 88
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1            #                           #    ###   #  ##  ## ###    
1MMS_A        82 AGIEKGSse---pKRKIVGKVTRKQIEEIAKTKMPdlNANSLEAAMKIIEGTAKSMGIEV 138
gi 67464170   86 KEPPKDRkknkgiPTVHSGSISMDDVYEIARTMRPrsLAKTFAGTVKEILGTCNSCGCQV 145
gi 121916871  81 NEPHRDRkk--tkAVKHSGSLSLDTIIDIARTMRAksCARKLAGTVKEVLGTAQAMGAHV 138
gi 3914677    81 AGASEPSgd---pAHKKIGNLSLEQVIKIAIMKKPglTTKSLKAALKSMLGTAKSIGLTV 137
gi 18313825   81 FGKDTGAhd---aRNEVIGNLSFAQLVEIALLKKDelKSKTLKSAVKQLLSTCKAMGVTV 137
gi 126465989  81 VGVKQPPgd---pAHQKIGDLPIDKIIKIAILKKEqlTAKTLKAAVKTILGTARSIGITV 137
gi 124028449  81 VGASEPSgd---pMHQKIGDLPFEKIVEIAILKKPslNAKTLKAAVKTILGSARSIGITV 137
gi 156937968  81 AGAKAPSgd---pIHQKVGDLPFEKVIEAALLKAPelTAKTLKGAVKTVLGTARAIGLTV 137
gi 145476333  86 GGYERDRkk--tkNVKHNGNLTLEQVIKVARAVEEksLAKTFTGTVKQVLGTAQSLGATV 143
gi 160948256  89 NEPQRDRkk--vkNVRHNGTITFDDVIDIARLLQPrsMSRQLVGTVKSVLGTCNSVGCLI 146

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