1PP8


Conserved Protein Domain Family
IBD

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pfam10416: IBD 
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Transcription-initiator DNA-binding domain IBD
In Trichomonas vaginalis, thought to be the earliest extant eukaryote, the sole initiator element for control of the start of transcription is Inr, and this is recognized by the initiator binding protein IBP39. IBP39 contains an N-terminal Inr binding domain, IBD, connected via a flexible, proteolytically sensitive, linker (residues 127-145) to a C-terminal domain. The IBD structure reveals a winged-helix-wing conformation with each element binding to DNA, the central helix-turn-helix contributing the majority of the specificity-determining contacts with the Inr core motif TCAPy(T/A). The binding of IBP39 to the Inr directly recruits RNA polymerase II and in this way initiates transcription.
Statistics
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PSSM-Id: 402166
View PSSM: pfam10416
Aligned: 94 rows
Threshold Bit Score: 53.9006
Threshold Setting Gi: 123320815
Created: 11-May-2020
Updated: 7-Aug-2020
Structure
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Program:
Drawing:
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
1PP8_V         6 LE--AS-FTSRLPPEIVAALKRKssRDPNSRFPRKLHMLLTYLASNPQLEEEIGLSWISDTeFKMKKKNVALVMGIKLNT 82  Trichomonas vag...
XP_001328439 108 PErwENvPTVEFSSLQSVYFPKR--SSKKLRFEQKLWNALLLTQKYPSLKPVIGVEWITNDvIRVEVNTLAKLLGISKAT 185 Trichomonas vag...
EAY20823     190 SLywPN-KDFLLGDIILDFFQRK--SNINCRFIHKLYNALRIVQIYPMLKELIGIEWISPNiLKVRKCCFARLLGIKSID 266 Trichomonas vag...
XP_001580233 162 SKfwPD-KNFAFGDIVADFFQRK--NNANCRFSHKLYNAIQISKNLPDLQIFTGVEWVGKYvLKVNKNRFARLLGIHSID 238 Trichomonas vag...
EAY20898     154 RRfwPN-ERILLRDLVTDYFRAD--PSPNSRFSHKLYNALQIVKKDPFYFLLFGVEWMNETvLKVNGPLFSCVLGLQNYK 230 Trichomonas vag...
EAX97463     119 ANywIA-EENTFGSLVTQFFQKK--NNSNCRFPHKLYNGLVLVEANPEMYPLVGLKWITDTvFKVDKYIFGRLLGITSIN 195 Trichomonas vag...
XP_001320292 134 AStwSS-DIITFGNLVQSFFRRR--NSSASKFPYKLFNALRITELYPEYFPHIGVKWVDDNiIWVSREPFARLIGVRTIE 210 Trichomonas vag...
XP_001583090 136 YSlwKS-ENITFGYLVSFHFRKR--NSSNSKFPIKLFNALKITEHCPDLFPHIGVKWITDDvIWVDREAFACLIGVKTVE 212 Trichomonas vag...
EAX97047      75 HDfwSHyKKISFENMIHTYFHRR--NSSHARFVYKLYNALLITAAYPSLLPMIGVSWETNNiIKVRKTPFASLIGTRIAD 152 Trichomonas vag...
XP_001319637 115 HDfwRRyETITFQQMVDVYFHKR--NSSPYRFTFKLYNALLLTEKYPNLLHLVGATWQTNKiLKIYKTPFSCLIGTRVAN 192 Trichomonas vag...
1PP8_V        83 -----LNVNLRDLAFE--QLQH--DKGGWTQWKRSGFTR 112 Trichomonas vaginalis
XP_001328439 186 salcsPQGSFPSHGFVeiVKQDggSYMFNNSENVRYYQH 224 Trichomonas vaginalis G3
EAY20823     267 gglfhKQGNFPSLGFRelTMDE--ANVYCQGLDISDVDY 303 Trichomonas vaginalis G3
XP_001580233 239 gslfhQQGNFSTHGFIevGGEE--A-----KRLIGEAEF 270 Trichomonas vaginalis G3
EAY20898     231 ynlfsQNGQMSIHGFIelNEKD--ALAYCNAETLQDIDF 267 Trichomonas vaginalis G3
EAX97463     196 gglvhSQGNFPSHGFKelNNEE--VMALKMKYSLKDVDM 232 Trichomonas vaginalis G3
XP_001320292 211 gglfhQQGNFPSHGFVelSFEE--SESVAAQHNLGHVAL 247 Trichomonas vaginalis G3
XP_001583090 213 gglfhQQGNFPSHGFVelSYEE--SQMLANSLNLGRIDL 249 Trichomonas vaginalis G3
EAX97047     153 nslfhKQGNFPTHGFAelTSEE--A--VVHNINISYIDF 187 Trichomonas vaginalis G3
XP_001319637 193 nslfhKQGNFPTHGFAelTTEE--A--LAKNIDIRQIDF 227 Trichomonas vaginalis G3
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