NCBI CDD Logo
?
cd01645: RT_Rtv 
Click on image for an interactive view with Cn3D
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.
BioAssay Targets and Results
?
CID: 732503
AID: 651
GI: 1431733
more
HIV-1 RT-RNase H MLSCN HTS MH077605 Confirmation Assay
Chemical Name: AC1LE9QF
CID: 732503
AID: 565
GI: 1431733
more
HIV-1 RT-RNase H MLSCN HTS MH077605
Chemical Name: AC1LE9QF
CID: 732503
AID: 652
GI: 1431733
more
HIV-1 RT-RNase H MLSCN MH077605 Probe Assessment: Dose response Assay
Chemical Name: AC1LE9QF
Statistics
?
PSSM-Id: 73152
View PSSM: cd01645
Aligned: 19 rows
Threshold Bit Score: -1
Threshold Setting Gi: 0
Created: 10-May-2006
Updated: 9-Mar-2011
Structure
?
Program:
Drawing:
Aligned Rows:
Hierarchy
?
Display:
 
Conserved site includes 29 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Structure:1RTD_A; HIV-1 RT binds DNA template:primer, TTP and two Mg ions; contacts at 3.5A.
    View structure with Cn3D
  • Citation:PMID 9831551

cd01645 is part of a hierarchy of related CD models.
Use the graphical representation to navigate this hierarchy.
cd00304:RT_likecd01644:RT_pepA17cd01645:RT_Rtvcd01646:RT_Bac_retron_Icd01647:RT_LTRcd01648:TERTcd01650:RT_nLTR_likecd01651:RT_G2_introncd01699:RNA_dep_RNAPcd01709:RT_like_1cd03487:RT_Bac_retron_IIcd03714:RT_DIRS1cd03715:RT_ZFREV_like1FKO A1RTD A1EP4 A1T05 A5198073546443329496260777913065138146070130635219132587107373520014733809347910504249260064051181119081181266741FKO A1RTD A1EP4 A1T05 A519807354644332949626077791306513814607013063521913258710737352001473380934791050424926006405118111908118126674
cd01645 Sequence Cluster
cd01645 Sequence Cluster
Sub-family Hierarchy
Click to see CD Hierarchy help
 cd01645 Branch
 Whole Hierarchy
 [Download CDTree]
CD Hierarchy
Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1               ##                                   #   #      # ### #  #       # ## #   
1FKO_A         18 GPKVKQWPLTEEKIKALVEICTEMekeGKISKigpenPYNTPVFAIKKKDstKWRKLVDFRELNKRTqDFWEVQLGIPHP 97
1RTD_A         18 GPKVKQWPLTEEKIKALVEICTEMekeGKISKigpenPYNTPVFAIKKKDstKWRKLVDFRELNKRTqDFWEVQLGIPHP 97
1T05_A         18 GPKVKQWPLTEEKIKALVEICTEMekeGKISKigpenPYNTPVFAIKKKDstKWRKLVDFRELNKRTqDFWEVQLGIPHP 97
1EP4_A         18 GPKVKQWPLTEEKIKALVEICTEMekeGKISKigpenPYNTPVFAIKKKDstKWRKLVDFRELNKRTqDFWEVQLGIPHP 97
gi 26006405   752 PVWIDQWPLTVEKLTVLKQLVNEQldnGHLEPsl--sPYNTPVFVIKKKSg-KWRLLHDLRAVNAIIkPMGALQCGLPNP 828
gi 52001473    33 PVWVNQWPLPKQKLEALHLLANEQlekGHIEPsf--sPWNSPVFVIQKKSg-KWHTLTDLRAVNAVIqPMGPLQPGLPSP 109
gi 464433     165 GPHVPQWPLTEEKLKGLTEIIDKLveeGKLGKapphwTCNTPIFCIKKKSg-KWRMLIDFRELNKQTeDLTEAQLGLPHP 243
gi 10504249    21 PVWLNQWPLKQEKLQALQQLVTEQlqlGHLEEsn--sPWNTPVFVIKKKSg-KWRLLQDLRAVNATMhDMGALQPGLPSP 97
gi 51980735   199 GPKIKQWPLSKEKIEALTEIVYRLekeGKVKRadpnnPWNTPIFCIKKKSg-KWRMLIDFRTLNELTeKGAEVQLGLPHP 277
gi 118126674    8 PVWIPQWLLTVEKLRVVNELVDRElkaGHLVEst--rPWNSPIFVIKKKSg-QWCLLHDLRGMNSTLqDMGALQPGLPLP 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                     ######                                   ## #  #                    
1FKO_A         98 AGLKKNksvTVLDVGDAYFSVPLDEDFRKYTAFTIPSinnetPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQnPD 177
1RTD_A         98 AGLKKKksvTVLDVGDAYFSVPLDEDFRKYTAFTIPSinnetPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQnPD 177
1T05_A         98 AGLKKKksvTVLDVGDAYFSVPLDEDFRKYTAFTIPSinnetPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQnPD 177
1EP4_A         98 AGLKKKksvTVLDVGDAYFSVPLDEDFRKYTAFTIPSinnetPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQnPD 177
gi 26006405   829 NLIPQSydmMIIDLKDCFFSIPLHPKDKHIFAFTVPAlnnsqPTSRYQWKVLPQGMLNSPTMCQYFVSQVLQPYRDKySS 908
gi 52001473   110 AMIPKDwplIIIDLKDCFFTIPLAEQDCEKFAFTIPAinnkePATRFQWKVLPQGMLNSPTICQTFVGRALQPVREKfSD 189
gi 464433     244 GGLQKKkhvTILDIGDAYFTIPLYEPYREYTCFTLLSpnnlgPCKRYYWKVLPQGWKLSPSVYQFTMQEILEDWIQQhPE 323
gi 10504249    98 VAVPKGweiIIIDLQDCFFNIKLHPEDCKRFAFSVPSpnfkrPYQRFQWKVLPQGMKNSPTLCQKCVDKAILTVRDKyQD 177
gi 51980735   278 AGLQERkqvTVLDIADAYFTIPLDPDYAPYTAFTLPKinnsgPGERFVWCGLPQGWVLSPLIYQSTLNNILKPFREQhPE 357
gi 118126674   85 SMIPDAwscLVVDLKDCFFSIPLHPDDCQHFAMTVPAvnnaaPSQRYHWVVLPQVMKNSPTICQMYVALALKEFRGCyLK 164
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
Feature 1              # ##                                           ##   
1FKO_A        178 IVIYQYMDDLYVGSDLeigQHRTKIEELRQHLLRwGLTTPDKKHQKeppFLWMGYEL 234
1RTD_A        178 IVIYQYMDDLYVGSDLeigQHRTKIEELRQHLLRwGLTTPDKKHQKeppFLWMGYEL 234
1T05_A        178 IVIYQYMDDLYVGSDLeigQHRTKIEELRQHLLRwGLTTPDKKHQKeppFLWMGYEL 234
1EP4_A        178 IVIYQYMDDLYVGSDLeigQHRTKIEELRQHLLRwGLTTPDKKHQKeppFLWMGYEL 234
gi 26006405   909 FLVYHYMDGILVATPGpkgTVLKTLPHLQRILQQgGLHIAPDKVQLsspFHYLGHKV 965
gi 52001473   190 CYIIHYIDDILCAAETk-dKLIDCYTFLQAEVANaGLAIASDKIQTstpFHYLGMQI 245
gi 464433     324 IQFGIYMDDIYIGSDLeikKHREIVKDLANYIAQyGFTLPEEKRQKgypAKWLGFEL 380
gi 10504249   178 SYIVHYMDDILLAHPSr-sIVDEILTSMIQALNKhGLVVSTEKIQKydnLKYLGTHI 233
gi 51980735   358 IDLYQYMDDIYIGSDLgkkEHKQIVEELRKLLLWwGFETPEDKLQEqppYKWMGYEL 414
gi 118126674  165 LLIYHYMDDILVAGRE---LPKDIERQLWHHLEEwGLRVGEDKTQQghpIQYLGVIV 218

Citing CDD
Marchler-Bauer A et al. (2013), "CDD: conserved domains and protein three-dimensional structure.", Nucleic Acids Res. 41(D1):D384-52.
| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
Click on image for an interactive view with Cn3D
Conserved site includes 29 residues -Click on image for an interactive view with Cn3D