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:
Feature 1         #                   #                                                ###   #   
1MMS_A         8 IKLQLPAGKATPappvGPALGQh--GVNIM-EFCKRFNAETADk-AGMILPVVITVYEd-kSFTFIIktPPASFLLKKA- 81  Thermotoga mari...
XP_648500     13 LVVKVVAGDAAAgaslGPKVGPl--GLNPK-KTGDDLAKSTLAw-KGLRVTVRITVVNr--VATYEVi-PSAAALILKAl 85  Entamoeba histo...
EAY21649       8 IKCRVWGGETGVtsklAPKLGPl--GVPAP-KVAQEVAKATEKf-KGFRATVKITVQNr--EFKVDVe-NSTSTLLIAAl 80  Trichomonas vag...
P96037         6 IKIMVEGGNVKPgpplAPTLSQl--GLNVG-EVVKKLNEATSSf-KGMSVPVTIEVDSstkKYEIKVgiPTTTALLLKE- 80  Sulfolobus solf...
NP_560492      6 VTVPLQGGKVAVnpqfQDALKQi--GLDPN-AVVQRVQEELKKvgKYPVQKVEVEVVSp-sKYEVKIylPPIGDLLLKL- 80  Pyrobaculum aer...
YP_001041098   6 IKVMVEGGKANPgpplGPTLSPl--RVNVM-EVVKAINEATKDf-EGLTVPVEIIVDTstrKFEVKVgiPTTTALLLKE- 80  Staphylothermus...
YP_001013769   6 INVKVRGGEAKPapplAPAIEKl--GLDVN-KVVEDINKATEKy-KGFEVAVKLIVDEntkEYEIEVkpPTTTELLLKA- 80  Hyperthermus bu...
YP_001435764   6 LTFSVEGGNAKPappiKPALESv--GLDPN-EVVQKINEVTKRy-KGFTVTVKVIVDPdtkEYEIEVepPNITELLLKL- 80  Ignicoccus hosp...
XP_001424189  13 INIKVFGGEGGPastlAPKLGPl--GLNPK-QVGDKIIAESGKw-KGIRVMVNLRCQNr--NADVTVi-PTSSALLIKEi 85  Paramecium tetr...
CAO94729      13 VFIKCRGGDILPeyllAPKFFGfdfRWNEIkFIAKEISDITRDy-KDLKVTIQFTVQNr--KAEMMVv-PTASSLIIKAl 88  Pomphorhynchus ...
Feature 1            #                           #    ###   #  ##  ## ###    
1MMS_A        82 AGIEKGSse---pKRKIVGKVTRKQIEEIAKTKMPdlNANSLEAAMKIIEGTAKSMGIEV 138 Thermotoga maritima
XP_648500     86 KEPPKDRkknkgiPTVHSGSISMDDVYEIARTMRPrsLAKTFAGTVKEILGTCNSCGCQV 145 Entamoeba histolytica HM-1:IMSS
EAY21649      81 NEPHRDRkk--tkAVKHSGSLSLDTIIDIARTMRAksCARKLAGTVKEVLGTAQAMGAHV 138 Trichomonas vaginalis G3
P96037        81 AGASEPSgd---pAHKKIGNLSLEQVIKIAIMKKPglTTKSLKAALKSMLGTAKSIGLTV 137 Sulfolobus solfataricus
NP_560492     81 FGKDTGAhd---aRNEVIGNLSFAQLVEIALLKKDelKSKTLKSAVKQLLSTCKAMGVTV 137 Pyrobaculum aerophilum str. IM2
YP_001041098  81 VGVKQPPgd---pAHQKIGDLPIDKIIKIAILKKEqlTAKTLKAAVKTILGTARSIGITV 137 Staphylothermus marinus F1
YP_001013769  81 VGASEPSgd---pMHQKIGDLPFEKIVEIAILKKPslNAKTLKAAVKTILGSARSIGITV 137 Hyperthermus butylicus DSM 5456
YP_001435764  81 AGAKAPSgd---pIHQKVGDLPFEKVIEAALLKAPelTAKTLKGAVKTVLGTARAIGLTV 137 Ignicoccus hospitalis KIN4/I
XP_001424189  86 GGYERDRkk--tkNVKHNGNLTLEQVIKVARAVEEksLAKTFTGTVKQVLGTAQSLGATV 143 Paramecium tetraurelia strain d4-2
CAO94729      89 NEPQRDRkk--vkNVRHNGTITFDDVIDIARLLQPrsMSRQLVGTVKSVLGTCNSVGCLI 146 Pomphorhynchus laevis

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