2NXP,2J49,2J4B


Conserved Protein Domain Family
TAF5_NTD2

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cd08044: TAF5_NTD2 
Click on image for an interactive view with Cn3D
TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated Factor 5 (TAF5), involved in forming Transcription Factor IID (TFIID)
The TATA Binding Protein (TBP) Associated Factor 5 (TAF5) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TAF5 contains three domains, two conserved sequence motifs at the N-terminal and one at the C-terminal region. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF5 may play a major role in forming TFIID and its related complexes. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. TAF5 has a paralog gene (TAF5L) which has a redundant function. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. C-terminus of TAF5 contains six WD40 repeats that likely form a closed beta propeller structure and may be involved in protein-protein interaction. The first part of the TAF5 N-terminal (TAF5_NTD1) homodimerizes in the absence of other TAFs. The second conserved N-terminal part of TAF5 (TAF5_NTD2) has an alpha-helical domain. One study has shown that TAF5_NTD2 homodimerizes only at high concentration of calcium but not any other metals. No dimerization was observed in other structural studies of TAF_NTD2. Several TAFs interact via histone-fold (HFD) motifs; HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamer. However, TAF5 does not have a HFD motif.
Statistics
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PSSM-Id: 176269
View PSSM: cd08044
Aligned: 67 rows
Threshold Bit Score: 89.5598
Threshold Setting Gi: 145606002
Created: 2-Oct-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Ca binding sitehomodimer
Conserved site includes 3 residues -Click on image for an interactive view with Cn3D
Feature 1:Ca binding site [ion binding site]
Evidence:
  • Comment:Biochemical and genetic studies suggest that calcium is not a key player in TAF5 assembly.
  • Structure:2NXP,: Human TAF5_NTD2 binds Ca(II) ion; contacts at 4.0 A
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                        #  ##            
2NXP_A         24 PTXYEEYYSGLKHFIECslDCHRAELSQLFYPLFVHXYLELVYnqhenEAKSFFEKFHGDqeCYYQDDLRVL-SSLTKKE 102  human
P49846        113 AQHYEQAYKELRTFVEDslDIYKHELSMVLYPILVQIYFKILAsglreKAKEFIEKYKCDldGYYIEGLFNL-LLLSKPE 191  fruit fly
Q9VT91        320 FADYEFAVKKLIKLIQStpSHYKYEIYILLYPLLVLTYLQMMAsdkiqKARMLLVRFQDHldDSYISRIIKL-REISKPA 398  fruit fly
XP_002132278  242 FEQYEQAFHAVLSMVEAvcDRFRYDISQLLYPLLVLAYLQMVAsdnvdGAATLVKNCGKYldDSYRPRLATL-KKILRPA 320  Drosophila ps...
XP_002069081  974 YKLYEATVLAIYKLTLEatSRFRYQFSTMLFPIFGLCYLLMIAsnkstEALTFIKRNQMYfnESEMGRIEKL-LKIKNAD 1052 Drosophila wi...
XP_001957804  660 FEEYEQAVHRLIRMVPKvpSHHRFEIHLMVYPMMAITYMQMVAgdnmqRAIDFLEKESCQlnESYTSRLTKL-ADICRLE 738  Drosophila an...
XP_002020757  123 YLEYQQTFLEIRKLVEEvpNEFKYEISALLYPMLVLGYLQMVVggdhkMAKRFLEENEDCleDIYDRSIAKL-RRIRRPQ 201  Drosophila pe...
XP_001984594  250 LNEYEELFHEIRKIIPKvpNRFKYEIYSLLFPTLTIVYFRMVIsgkfrKGRAFVESSRRYfdHSYTARVDKLlGMQDPRD 329  Drosophila gr...
XP_002047833   82 LNDYEQLFHEIRKIIDRvpNRFKYEIYNLLYPTLAVVYLRMISsgkyrKGKAFVESCLRYidHSYMARVDKLmVLQTPGD 161  Drosophila vi...
XP_001901002   55 NDSIMREFSTLLSHIDSsfDNFRAELSALIFPVFAHLYIQLIAegrslQAALFGEKFSRYvpSMYEEQTKLL-TRISTHS 133  agent of lymp...
Feature 1                                                                
2NXP_A        103 HXKGNETXLDFRTSKFVLRISRDSYQLLKRHLQekQNNQIWNIVQEH-LYIDIFD 156  human
P49846        192 ELLENDLVVAMEQDKFVIRMSRDSHSLFKRHIQdrRQEVVADIVSKY-LHFDTYE 245  fruit fly
Q9VT91        399 EVPNKARKLLAGLEKVKIEMSEGAFRQLLLCTEewTRGQQEKLLSHFqIQPYSED 453  fruit fly
XP_002132278  321 EVPSRARVLLNGHYKVDILMTRDAYTQCLIHLAriPFWQQDKIMGHIrLRKYDDE 375  Drosophila pseudoobscura pseudoobscura
XP_002069081 1053 SVPKKAKSILSGWEKIEIRISLPAYKQSLLYIEdwPIEQQRMVLSLFfFNCYEEN 1107 Drosophila willistoni
XP_001957804  739 DIPNKARKQLAGYEKLELHMSKGAFRQLLFQLEewPRSHQEKVLTHFrILSYSED 793  Drosophila ananassae
XP_002020757  202 QVPGRALELLLRRDLVRIEMPQAASIKFSEYRAkwPLDQQNVFIGHIaIDDLETA 256  Drosophila persimilis
XP_001984594  330 IPHKARKLVTDDKEKVRFSMFKETYYLLEIHRNfwRLPIQMMFSKHFePFPDNKN 384  Drosophila grimshawi
XP_002047833  162 MPIKARKLISDENAQVPVSMFEETYYVLLLCMEswSRSLQMTFIRHFdLFPDYNN 216  Drosophila virilis
XP_001901002  134 QAVNHALVQALTKNQFVVRISKSAIKQLEPFLT--RNSTVRDVMRDH-LHIEAID 185  agent of lymphatic filariasis

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