1FA0,2IKF,1Q79


Conserved Protein Domain Family
NT_PAP_TUTase

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cd05402: NT_PAP_TUTase 
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Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases.
Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxylate residues are conserved.
Statistics
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PSSM-Id: 143392
View PSSM: cd05402
Aligned: 129 rows
Threshold Bit Score: 59.4931
Threshold Setting Gi: 134104550
Created: 16-Jun-2007
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 15 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:Active site includes residues involved in ATP and metal-binding (from structural studies), and primer-binding (from mutagenesis and kinetic studies).
  • Structure:1Q79_A, Bos taurus PAP bound with an ATP analog (3'- dATP) and manganese ions, contacts determined at 4A.
    View structure with Cn3D
  • Structure:1FA0_A,Yeast PAP bound with an ATP analog (3'- dATP) and manganese ions, contacts determined at 4A.
    View structure with Cn3D
  • Structure:2IKF_A, Trypanosoma brucei TUTase4 bound with UTP and a magnesium ion, contacts determined at 4A.
    View structure with Cn3D
  • Comment:TUTases may use the same two-metal mechanism as others in the NT superfamily.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                 ###         ## #                        
1FA0_A         47 NRVQVLKILQELAQrfvyevskkknmsdgmardAGGKIFTYGSYRLGVHGPGSDIDTLVVvpkh---------------- 110
1Q79_A         60 RRILILGKLNNLVKewireisesknlpqsvienVGGKIFTFGSYRLGVHTKGADIDALCVaprh---------------- 123
gi 57863246   375 VRQEIVEEMSKVITtf----------------lPECSLRLYGSSLTRFALKSSDVNIDIKfppk---------------- 422
gi 116500700   65 LRRDLVSRFVKLVDkl----------------dPDATVRVLGSTASGLHYPTSDIDMTITfrgvsks------------- 115
gi 42565594    63 TRKELVKNLNTMALdiyg-----------kseeSSPVLEAYGSFVMDMYSSQSDLDVSINfgngtse------------- 118
gi 47226593    82 KRRSVVAVMQDLLLsv----------------lPEIRLRLYGSSCTKFGFKDSDVNIDIQfpqh---------------- 129
gi 67462099   315 QRLEIKRVMESVFRhk----------------lPDCSLRLYGSSCSRLGFRDSDVNIDVQfpav---------------- 362
gi 114797027   30 MRTRLIDSIQGALKhri--------------gvQDLHVQPYGSFVSQQYNAGSDLDLALCgyipaaklkpaalaeiyrge 95
gi 74582471    40 YRKLLLEKLQTHIRev----------------vLDAELQVYGSMYIGTTLSISDVDVSLKspr----------------- 86
gi 68126274    24 IDKEVVDDLRLRVVdlcs------------rcvNKVELQLFGSLATGFCTTGADADLSLTfrnfspwl------------ 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                     ## # #          #                   
1FA0_A        111 ------vtrEDFFTVFDSLLRERke---------lDEIAPVPDAFVPIIKIKFs--GISIDLICArldqpqvplsltlsd 173
1Q79_A        124 ------vdrSDFFTSFYDKLKLQee---------vKDLRAVEEAFVPVIKLXFd--GIEIDILFArlalqtipedldlrd 186
gi 57863246   423 ------mnhPDLLIKVLGILKKNvl---------yVDVESDFHAKVPVVVCRDrksGLLCRVSAGn-------------- 473
gi 116500700  116 --ssrssstRTRLSTLEHKIQSSgf---------aSRIDSILNAAVPLLRITDamtGLEIDLTASd-------------- 170
gi 42565594   119 ---iprekkLEILKRFAKKLRSLqge------gqvKNVESIFSAKVPIVKFSDqgtGVECDLSVEn-------------- 175
gi 47226593   130 ------mhqPDVLLLVKETLSVCpl---------fVDVEADFHARVPVVLCKDktcGLICKVSAGn-------------- 180
gi 67462099   363 ------msqPDVLLLVQECLKNSds---------fIDVDADFHARVPVVVCRDkqsGLLCKVSAGn-------------- 413
gi 114797027   96 peeelvplhKLDKRTKANLLRDAgyrlagsgvasrDSMEFVLHARVPIVKFADratGIEVDLCLGnaatsfk-------- 167
gi 74582471    87 -------vgELEKRRVTMVLRKYl----------dADADFHSSARVPRINLVDv-sGIGVDLTFGn-------------- 134
gi 68126274    80 --sgieavdAQNFKRLARVGREAge--------mgMKNVRLINACIPVVHFQDavsGIRCDLSIGn-------------- 135
                         170       180
                  ....*....|....*....|....*...
Feature 1                        ##  ##       
1FA0_A        174 knllrnldekdlralNGTRVTDEILELV 201
1Q79_A        187 dsllknldirxirslNGCRVTDEILHLV 214
gi 57863246   474 --------------dMACLTTDLLTALG 487
gi 116500700  171 --------------eRGVKGTKMVLAWT 184
gi 42565594   176 --------------kDGILNSQIVRIIS 189
gi 47226593   181 --------------eNAYQTTAYLAALS 194
gi 67462099   414 --------------eNAWLTTKHLTALG 427
gi 114797027  168 ---------awsvarVAEINPAFGRLYK 186
gi 74582471   135 --------------dKACRTAELQKAYN 148
gi 68126274   136 --------------vNGVANSKILAEIH 149

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