1WB3


Conserved Protein Domain Family
SelB_euk

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cd01889: SelB_euk (this model, PSSM-Id:133289 is obsolete and has been replaced by 206676)
Click on image for an interactive view with Cn3D
SelB subfamily. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryotes, they do share a common feature. Unlike in E. coli, these SECIS elements are located in the 3' UTRs. This group contains eukaryotic SelBs and some from archaea.
Statistics
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PSSM-Id: 133289
View PSSM: cd01889
Aligned: 16 rows
Threshold Bit Score: -1
Threshold Setting Gi: 0
Created: 30-Apr-2009
Updated: 9-Mar-2011
Structure
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Program:
Drawing:
Aligned Rows:
  next features
Conserved site includes 12 residues -Click on image for an interactive view with Cn3D
Feature 1:GTP/Mg2+ binding site [chemical binding site]
Evidence:
  • Comment:Based on sequence similarity with elongation factor EF-Tu.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1              ######                                                                 
1WB3_D     20 INLGIFGHIDHGKTTLSKVLTEIASTSAHDKLPESQKRGITIDIGFSAFKle---------------------------- 71   Methanococcus mar...
NP_247471  10 VNVGLFGHIDHGKTQLAKQLTEIASTSALDKPKESQKRGITIDLGFSSFTld---------------------------- 61   Methanocaldococcu...
NP_703302   4 INVGVLGHVDSGKTSLCKCLSQVLSTCALDKHKESKERGITIDLGFSSFYikkkkkkkydvnqkreiqtnllndqttdqk 83   Plasmodium falcip...
XP_746090   4 VNIGVLGHVDSGKTSLCRCLSEVLSTCALDKHRQSQEKGITIDLGFSSFYikkkksqittsqnqheetqnnkiipkhest 83   Plasmodium chabau...
XP_646756  39 FNIGIMGHVDSGKTSLAKALSTNLSTASLDKSPASQERGITLDLGFSSFQikkdklaenn-------------------- 98   Dictyostelium dis...
AAX27281   11 INVGVLGHVDSGKTSLAKVLSTVASTSAFDKNPQSKKRGITLDLGFSSFIvnsasypfep-------------------- 70   Schistosoma japon...
EAL26649    5 FNVGLLGHVDSGKTTLARALSSISSTAAFDKNPQSVDRGITLDLGFSGLLvdappnl----------------------- 61   Drosophila pseudo...
EAA10761    5 LNIGILGHVDSGKTTLARALSAIASTAAFDKNPQSQERGITLDLGFSALQvdlpdhlreq-------------------- 64   Anopheles gambiae...
CAJ08005    4 VNIGLLGHVDSGKTALAKALSSTASTAAFDKSPQSQSRGITLDLGFSACEvsvedgnedat------------------- 64   Leishmania major
AAX79739   12 INIGILGHVDSGKTSLARALSSTASTAAFDKSPESQRRGITLDLGFSATCvptegiapd--------------------- 70   Trypanosoma brucei
Feature 1                                                                                     
1WB3_D     72 ---------------------------------------------------nyRITLVDAPGHADLIRAVVSAADIIDLA 100  Methanococcus mar...
NP_247471  62 ---------------------------------------------------ryRITLVDAPGHSELIRTAIGAGNIIDAA 90   Methanocaldococcu...
NP_703302  84 esflyckreekndlhniqydktnieyneeqncydytndkhhsnniyfydeeiiQICLVDCPGHHSLLKSIIMGSEITDII 163  Plasmodium falcip...
XP_746090  84 andne--------------nqndvkredinndceegniqnknisnenpedeliQICLVDCPGHHSLIKCIVMGAKIMDMI 149  Plasmodium chabau...
XP_646756  99 -------------------------------------------nnnndnnnniQITLVDCPGHASLIKTIIGGSQIIDMM 135  Dictyostelium dis...
AAX27281   71 --------------------------------------------sihqnfenvQFTLVDCPGHGSLIRTVLCGSQIIDVV 106  Schistosoma japon...
EAL26649   62 -----------------------------------------------pqtdklQFTFVDCPGHASLIRTIIGGAQIIDLM 94   Drosophila pseudo...
EAA10761   65 --------------------------------------------aiaegyeklQYTFVDCPGHASLIRTIIGGAQIIDMM 100  Anopheles gambiae...
CAJ08005   65 ------------------------------------------qvlraaeltkvQCTLVDCPGHASLIRTVVGGAQIIDAM 102  Leishmania major
AAX79739   71 --------------------------------------------lfnagiqqvQCTFVDCPGHASLIRTVLGGAQIIDMM 106  Trypanosoma brucei
Feature 1                                     ## #                                         ###
1WB3_D    101 LIVVDAKEGPKTQTGEHMLILDHFNiPIIVVITKSDNAGte---eIKRTEMIMKSILqsth------nlknSSIIPISAK 171  Methanococcus mar...
NP_247471  91 LLVVDAKEGPKTQTGEHLLVLDLLNiPTIVVINKIDIANde---eIKRTEMFMKQILnsti------nlknSKIIKISAK 161  Methanocaldococcu...
NP_703302 164 ILVIDINKGIQKQTIECLVLCKIINcDIIIVLNKIDLIPlh---lREKKINLMKKKIqeafykfkslqslnYHIVSISAN 240  Plasmodium falcip...
XP_746090 150 FLVIDINKGIQKQTIECLVLCQFVKsDIIIILNKIDLIPlh---eRDKKINSMKKKIkdainkt-slkklsYYIVSLSAN 225  Plasmodium chabau...
XP_646756 136 FLVIDIVKGIQTQTAECIVIGEITCkKGIIILNKIDQIPve---sRKEKIEQVSSKLrkalek---tcfkdSLIIPFSAT 209  Dictyostelium dis...
AAX27281  107 ILVVDVTKGFQTQTAECLVIGEITCkKMLVVLNKCDLLDid---qRCELIQKMRKRIlktlen---tifkqSKIAEISAA 180  Schistosoma japon...
EAL26649   95 LLVVDAQKGIQTQTAECLVIGELLQkKLIVVINKIDAFAta---qREIKLEKLRARLvktlaa--tsfgseVPMYAVSAL 169  Drosophila pseudo...
EAA10761  101 LLVIDAEKGIQPQTAECLLIGELTCrKMIVVLNKVDALQdp--aqRTKTLDRLRKGIagvlsk---msfdaSPIVAISAS 175  Anopheles gambiae...
CAJ08005  103 VLVVDATKGIQVQTAECLVLGEVLAkPLVVVLNKIDAIQgvspagKEAALAALKRKLqqvfrr---trwptVAIVEVAAA 179  Leishmania major
AAX79739  107 ILVIDACKGIQTQTAECIVIGEVLCkPLVLVINKVDAIQgstseeKRAAIDKLRKRLqktfer---trwpsVAMVEVAAA 183  Trypanosoma brucei
Feature 1                                   
1WB3_D    172 TGfg-----------vdELKNLIITTLNNA 190  Methanococcus maripaludis
NP_247471 162 TGegig-------elkkELKNLLDSLDIKR 184  Methanocaldococcus jannaschii DSM 2661
NP_703302 241 VKgkd----------nkDVEGDPPNLLSHD 260  Plasmodium falciparum 3D7
XP_746090 226 SKnt-----------ggDEMGEKTHSMCGD 244  Plasmodium chabaudi chabaudi
XP_646756 210 GGsss---------gggSNSNKIEPIGIDL 230  Dictyostelium discoideum AX4
AAX27281  181 PGgiqvef----tseqrTNNSQEVENLITL 206  Schistosoma japonicum
EAL26649  170 EGiyip-------elraGLSDAYFQPQRNV 192  Drosophila pseudoobscura
EAA10761  176 TGenvs-------alvdTMNGKSFMPQRDM 198  Anopheles gambiae str. PEST
CAJ08005  180 PRevag-------gighPVNTEAVLPQVLR 202  Leishmania major
AAX79739  184 PRreesggttcegcmmsPINVEKVLPAVLS 213  Trypanosoma brucei

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