2EXU


Conserved Protein Domain Family
Spt4

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cd07973: Spt4 
Click on image for an interactive view with Cn3D
Transcription elongation factor Spt4
Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 complex. Spt4 homolog is not found in bacteria.
Statistics
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PSSM-Id: 153422
View PSSM: cd07973
Aligned: 33 rows
Threshold Bit Score: 86.9089
Threshold Setting Gi: 154344803
Created: 3-Oct-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Spt4-Spt5NGNZn binding site
Conserved site includes 7 residues -Click on image for an interactive view with Cn3D
Feature 1:Spt4-Spt5NGN interface
Evidence:
  • Comment:The Spt4-Spt5 interface is held by alignment of their beta sheets and an Acid-Dipole interaction
  • Comment:Direct backbone contacts are formed between beta3 of Spt4 and beta2 of Spt5NGN
  • Comment:Hydrogen bond between the conserved Ser in Spt4 and Glu in Spt5NGN results in a strong acid-dipole interaction

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                         ######    #                    
2EXU_A         2 SSERACMLCGIVQTTNEFNRDGCPNCq-GIFEEAGvst--meCTSPSFEGLVGMCKPTKSWVAKWLSVD-HSIAGMYAIK 77  baker's yeast
XP_001568343  27 GRYYACRRCRRILSEAQWYATGCVECs-AAMGIPDrdn-lldFATPHFHNFIGLIAPGQSWVARLIMKNrEPTNGIFAET 104 Leishmania braz...
EER17995      30 HQLRCCLRCHIILSVSQFVRHGCPNC--QDIDMEGdktlvedYTTKNFSGGVSVMNPSRSWVARQLKLS-TFCAGMYAVA 106 Perkinsus marin...
XP_002287639   8 KGVRACMRCGIIKTLDQFLEYGCENC--PFLDMAGnhercnlCTTAFFEGQVAVMDPSESWTAKWIRID-AYLPGVYAIS 84  Thalassiosira p...
XP_001743614  13 KHLRACLSCGLVKTSDQFFETGCENC--AYLDLNDnndaidsCTTARFYGIVSVIDPSDSWVAKWQGND-ACVPGCYALR 89  Monosiga brevic...
Q8LCQ3        14 HELRACLRCRLVKTYDQFRDSGCENC--PFFKIEDdherivdVTTPNFNGIISMMDPRRSWAARWLRIG-KFAPGCYTLA 90  thale cress
ABK26260      13 RELRACLRCRLIKTYDQFRETGCENC--PAFNMDQdhdrvvdCTTSNFSGIISCMDPTRSWSARWLRIS-RFVPGCYTLA 89  Sitka spruce
XP_813291     77 RGYLACRQCRLILTETQFIRDGCSVCgtGPVSRDElh----dVTTADFSNFVGLIAPEKSWVARMIGRT-GCPNGVFAAM 151 Trypanosoma cru...
XP_827569    135 HGYLACRRCRLIITEQQFLHEGCQVCgtGPVSREEll----dVATAEFSNFIGLIAPEKSWVGRLINRT-NCPNGVFATE 209 Trypanosoma bru...
XP_657505     31 NTLRCCKICGLIKSQEQFQRDGCDNCk-RYFDNWEd------YVSSNFTGMLSLLRPDRSFIGKVLGMKdTYVCGLYAAS 103 Entamoeba histo...
Feature 1                            
2EXU_A        78 VDGRLPAEVVELLPHYKPRD 97  baker's yeast
XP_001568343 105 LSDDEPEEEEDEMEPFVRGA 124 Leishmania braziliensis MHOM/BR/75/M2904
EER17995     107 AQGDGEAQGPYAWFDRSIID 126 Perkinsus marinus ATCC 50983
XP_002287639  85 VTGQFDRDIEEELENRGCRW 104 Thalassiosira pseudonana CCMP1335
XP_001743614  90 LQGHLPSDKLDEMPPNLRLR 109 Monosiga brevicollis MX1
Q8LCQ3        91 VSEALPEEMQFICQQARVQY 110 thale cress
ABK26260      90 VSEALSEEMQAVCEDNNVQY 109 Sitka spruce
XP_813291    152 LNDEDEEEIDSNDDGDDGAV 171 Trypanosoma cruzi strain CL Brener
XP_827569    210 LCDEDESGEEEEEVEENDVY 229 Trypanosoma brucei TREU927
XP_657505    104 CEDSVSPEIESTATVNDIQV 123 Entamoeba histolytica HM-1:IMSS

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