Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
E [auth A]SCOP2B SuperfamilyRibonuclease H-like 8075088 3000143 SCOP2B (2022-06-29)
G [auth C]SCOP2B SuperfamilyRibonuclease H-like 8075088 3000143 SCOP2B (2022-06-29)
F [auth B]SCOP2B SuperfamilyNucleotide cyclase/DNA polymerase palm domain-like 8036908 3001272 SCOP2B (2022-06-29)
F [auth B]SCOP2B SuperfamilyNucleotide cyclase/DNA polymerase palm domain-like 8036908 3001272 SCOP2B (2022-06-29)
H [auth D]SCOP2B SuperfamilyNucleotide cyclase/DNA polymerase palm domain-like 8036908 3001272 SCOP2B (2022-06-29)
H [auth D]SCOP2B SuperfamilyNucleotide cyclase/DNA polymerase palm domain-like 8036908 3001272 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
E [auth A]RVT_thumbe1rtdA7 A: alpha bundlesX: helical bundle domain in reverse transcriptase-like polymerases (From Topology)H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)T: helical bundle domain in reverse transcriptase-like polymerasesF: RVT_thumbECOD (1.6)
E [auth A]RVT_1e1rtdA8 A: a+b two layersX: Alpha-beta plaitsH: Adenylyl and guanylyl cyclase catalytic domain-likeT: Adenylyl and guanylyl cyclase catalytic domain-likeF: RVT_1ECOD (1.6)
E [auth A]RNase_He1rtdA6 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: RNase_HECOD (1.6)
E [auth A]RVT_connecte1rtdA5 A: mixed a+b and a/bX: Ribonuclease H-likeH: RNaseH-like domain in reverse transcriptase (From Topology)T: RNaseH-like domain in reverse transcriptaseF: RVT_connectECOD (1.6)
G [auth C]RVT_thumbe1rtdC7 A: alpha bundlesX: helical bundle domain in reverse transcriptase-like polymerases (From Topology)H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)T: helical bundle domain in reverse transcriptase-like polymerasesF: RVT_thumbECOD (1.6)
G [auth C]RVT_1e1rtdC8 A: a+b two layersX: Alpha-beta plaitsH: Adenylyl and guanylyl cyclase catalytic domain-likeT: Adenylyl and guanylyl cyclase catalytic domain-likeF: RVT_1ECOD (1.6)
G [auth C]RNase_He1rtdC6 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: RNase_HECOD (1.6)
G [auth C]RVT_connecte1rtdC5 A: mixed a+b and a/bX: Ribonuclease H-likeH: RNaseH-like domain in reverse transcriptase (From Topology)T: RNaseH-like domain in reverse transcriptaseF: RVT_connectECOD (1.6)
F [auth B]RVT_thumbe1rtdB3 A: alpha bundlesX: helical bundle domain in reverse transcriptase-like polymerases (From Topology)H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)T: helical bundle domain in reverse transcriptase-like polymerasesF: RVT_thumbECOD (1.6)
F [auth B]RVT_1e1rtdB2 A: a+b two layersX: Alpha-beta plaitsH: Adenylyl and guanylyl cyclase catalytic domain-likeT: Adenylyl and guanylyl cyclase catalytic domain-likeF: RVT_1ECOD (1.6)
F [auth B]RVT_connecte1rtdB1 A: mixed a+b and a/bX: Ribonuclease H-likeH: RNaseH-like domain in reverse transcriptase (From Topology)T: RNaseH-like domain in reverse transcriptaseF: RVT_connectECOD (1.6)
H [auth D]RVT_thumbe1rtdD1 A: alpha bundlesX: helical bundle domain in reverse transcriptase-like polymerases (From Topology)H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)T: helical bundle domain in reverse transcriptase-like polymerasesF: RVT_thumbECOD (1.6)
H [auth D]RVT_1e1rtdD2 A: a+b two layersX: Alpha-beta plaitsH: Adenylyl and guanylyl cyclase catalytic domain-likeT: Adenylyl and guanylyl cyclase catalytic domain-likeF: RVT_1ECOD (1.6)
H [auth D]RVT_connecte1rtdD3 A: mixed a+b and a/bX: Ribonuclease H-likeH: RNaseH-like domain in reverse transcriptase (From Topology)T: RNaseH-like domain in reverse transcriptaseF: RVT_connectECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
E [auth A],
G [auth C]
PF06817Reverse transcriptase thumb domain (RVT_thumb)Reverse transcriptase thumb domainThis domain is known as the thumb domain. It is composed of a four helix bundle [1].Domain
E [auth A],
G [auth C]
PF06815Reverse transcriptase connection domain (RVT_connect)Reverse transcriptase connection domainThis domain is known as the connection domain. This domain lies between the thumb and palm domains [1].Domain
E [auth A],
G [auth C]
PF00075RNase H (RNase_H)RNase HRNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.Domain
E [auth A],
G [auth C]
PF00078Reverse transcriptase (RNA-dependent DNA polymerase) (RVT_1)Reverse transcriptase (RNA-dependent DNA polymerase)A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs ...A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.
Domain
F [auth B],
H [auth D]
PF06817Reverse transcriptase thumb domain (RVT_thumb)Reverse transcriptase thumb domainThis domain is known as the thumb domain. It is composed of a four helix bundle [1].Domain
F [auth B],
H [auth D]
PF06815Reverse transcriptase connection domain (RVT_connect)Reverse transcriptase connection domainThis domain is known as the connection domain. This domain lies between the thumb and palm domains [1].Domain
F [auth B],
H [auth D]
PF00078Reverse transcriptase (RNA-dependent DNA polymerase) (RVT_1)Reverse transcriptase (RNA-dependent DNA polymerase)A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs ...A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth E],
C [auth G]
DNA TEMPLATE FOR REVERSE TRANSCRIPTASE---
B [auth F],
D [auth H]
DNA PRIMER FOR REVERSE TRANSCRIPTASE---
E [auth A],
G [auth C]
PROTEIN (REVERSE TRANSCRIPTASE)
F [auth B],
H [auth D]
PROTEIN (REVERSE TRANSCRIPTASE)

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
E [auth A],
G [auth C]
IPR036397Ribonuclease H superfamilyHomologous Superfamily
E [auth A],
G [auth C]
IPR043128Reverse transcriptase/Diguanylate cyclase domainHomologous Superfamily
E [auth A],
G [auth C]
IPR001995Peptidase A2A, retrovirus, catalyticDomain
E [auth A],
G [auth C]
IPR001878Zinc finger, CCHC-typeDomain
E [auth A],
G [auth C]
IPR008919Retrovirus capsid, N-terminalHomologous Superfamily
E [auth A],
G [auth C]
IPR012344Matrix protein, lentiviral and alpha-retroviral, N-terminalHomologous Superfamily
E [auth A],
G [auth C]
IPR036862Integrase, C-terminal domain superfamily, retroviralHomologous Superfamily
E [auth A],
G [auth C]
IPR018061RetropepsinsDomain
E [auth A],
G [auth C]
IPR010661Reverse transcriptase thumbDomain
E [auth A],
G [auth C]
IPR002156Ribonuclease H domainDomain
E [auth A],
G [auth C]
IPR036875Zinc finger, CCHC-type superfamilyHomologous Superfamily
E [auth A],
G [auth C]
IPR003308Integrase, N-terminal zinc-binding domainDomain
E [auth A],
G [auth C]
IPR001584Integrase, catalytic coreDomain
E [auth A],
G [auth C]
IPR045345Retroviral nucleocapsid Gag protein p24, C-terminal domainDomain
E [auth A],
G [auth C]
IPR010999Retroviral matrix proteinHomologous Superfamily
E [auth A],
G [auth C]
IPR021109Aspartic peptidase domain superfamilyHomologous Superfamily
E [auth A],
G [auth C]
IPR001969Aspartic peptidase, active siteActive Site
E [auth A],
G [auth C]
IPR012337Ribonuclease H-like superfamilyHomologous Superfamily
E [auth A],
G [auth C]
IPR017856Integrase-like, N-terminalHomologous Superfamily
E [auth A],
G [auth C]
IPR000071Immunodeficiency lentiviral matrix, N-terminalDomain
E [auth A],
G [auth C]
IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
E [auth A],
G [auth C]
IPR001037Integrase, C-terminal, retroviralDomain
E [auth A],
G [auth C]
IPR034170Retropepsin-like catalytic domainDomain
E [auth A],
G [auth C]
IPR000477Reverse transcriptase domainDomain
E [auth A],
G [auth C]
IPR010659Reverse transcriptase connectionDomain
E [auth A],
G [auth C]
IPR008916Retrovirus capsid, C-terminalHomologous Superfamily
F [auth B],
H [auth D]
IPR036397Ribonuclease H superfamilyHomologous Superfamily
F [auth B],
H [auth D]
IPR043128Reverse transcriptase/Diguanylate cyclase domainHomologous Superfamily
F [auth B],
H [auth D]
IPR001995Peptidase A2A, retrovirus, catalyticDomain
F [auth B],
H [auth D]
IPR001878Zinc finger, CCHC-typeDomain
F [auth B],
H [auth D]
IPR008919Retrovirus capsid, N-terminalHomologous Superfamily
F [auth B],
H [auth D]
IPR012344Matrix protein, lentiviral and alpha-retroviral, N-terminalHomologous Superfamily
F [auth B],
H [auth D]
IPR036862Integrase, C-terminal domain superfamily, retroviralHomologous Superfamily
F [auth B],
H [auth D]
IPR018061RetropepsinsDomain
F [auth B],
H [auth D]
IPR010661Reverse transcriptase thumbDomain
F [auth B],
H [auth D]
IPR002156Ribonuclease H domainDomain
F [auth B],
H [auth D]
IPR036875Zinc finger, CCHC-type superfamilyHomologous Superfamily
F [auth B],
H [auth D]
IPR003308Integrase, N-terminal zinc-binding domainDomain
F [auth B],
H [auth D]
IPR001584Integrase, catalytic coreDomain
F [auth B],
H [auth D]
IPR045345Retroviral nucleocapsid Gag protein p24, C-terminal domainDomain
F [auth B],
H [auth D]
IPR010999Retroviral matrix proteinHomologous Superfamily
F [auth B],
H [auth D]
IPR021109Aspartic peptidase domain superfamilyHomologous Superfamily
F [auth B],
H [auth D]
IPR001969Aspartic peptidase, active siteActive Site
F [auth B],
H [auth D]
IPR012337Ribonuclease H-like superfamilyHomologous Superfamily
F [auth B],
H [auth D]
IPR017856Integrase-like, N-terminalHomologous Superfamily
F [auth B],
H [auth D]
IPR000071Immunodeficiency lentiviral matrix, N-terminalDomain
F [auth B],
H [auth D]
IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
F [auth B],
H [auth D]
IPR001037Integrase, C-terminal, retroviralDomain
F [auth B],
H [auth D]
IPR034170Retropepsin-like catalytic domainDomain
F [auth B],
H [auth D]
IPR000477Reverse transcriptase domainDomain
F [auth B],
H [auth D]
IPR010659Reverse transcriptase connectionDomain
F [auth B],
H [auth D]
IPR008916Retrovirus capsid, C-terminalHomologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

ChainsEnzyme NameDescriptionCatalytic Residues
HIV-1 reverse transcriptase  M-CSA #1000

HIV-1 reverse transcriptase (RT) is a component of gag-pol polyprotein encoded by the human immunodeficiency virus-1 (HIV-1) genome. HIV-1 reverse transcriptase contains both DNA polymerase and ribonuclease H (RNase H) activities to convert the viral genomic RNA to double-stranded DNA, which is then integrated into the host genome and replicated along with the infected host cells. Understanding the HIV-1 reverse transcriptase catalytic mechanism is key for discovery of potent drugs and development of more effective, less toxic drugs and multi-drug combinations.

Defined by 5 residues: ASP:E-110 [auth A-110]VAL:E-111 [auth A-111]ASP:E-185 [auth A-185]ASP:E-186 [auth A-186]LYS:E-220 [auth A-220]
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