CATH Domain 3nfaA00

CATH Classification

Level	CATH Code	Description
	3	Alpha Beta
	3.30	2-Layer Sandwich
	3.30.420	Nucleotidyltransferase; domain 5
	3.30.420.10	Ribonuclease H-like superfamily/Ribonuclease H

Domain Context

CATH Clusters

Superfamily	Ribonuclease H-like superfamily/Ribonuclease H
Functional Family	POL polyprotein

Enzyme Information

2.7.7.7	DNA-directed DNA polymerase. based on mapping to UniProt P12497 Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). -!- Catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time. -!- Cannot initiate a chain de novo. -!- Requires a primer which may be DNA or RNA. -!- See also EC 2.7.7.49.
3.1.13.2	Exoribonuclease H. based on mapping to UniProt P12497 3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. -!- This is a secondary reaction to the RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end performed by EC 3.1.26.13.
3.4.23.16	HIV-1 retropepsin. based on mapping to UniProt P12497 Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro. -!- Present in human immunodeficiency virus type 1. -!- Contributes to the maturation of the viral particle, and is a target of antiviral drugs. -!- Active enzyme is a dimer of identical 11-kDa subunits. -!- Similar enzymes occur in other retroviruses. -!- Belongs to peptidase family A2.
2.7.7.-	Nucleotidyltransferases. based on mapping to UniProt P12497
2.7.7.49	RNA-directed DNA polymerase. based on mapping to UniProt P12497 Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). -!- Catalyzes RNA-template-directed extension of the 3'-end of a DNA strand by one deoxynucleotide at a time. -!- Cannot initiate a chain de novo. -!- Requires a RNA or DNA primer. -!- DNA can also serve as template. -!- See also EC 2.7.7.7.
3.1.-.-	Acting on ester bonds. based on mapping to UniProt P12497
3.1.26.13	Retroviral ribonuclease H. based on mapping to UniProt P12497 Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus. -!- Retroviral reverse transcriptase is a multifunctional enzyme responsible for viral replication. -!- To perform this task the enzyme combines two distinct activities. -!- The polymerase domain (EC 2.7.7.49) occupies the N-terminal two- thirds of the reverse transcriptase whereas the ribonuclease H domain comprises the C-terminal remaining one-third. -!- The RNase H domain of Moloney murine leukemia virus and Human immunodeficiency virus display two metal binding sites.

UniProtKB Entries (1)

POL_HV1N5

Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)

Gag-Pol polyprotein

PDB Structure

PDB	3NFA
External Links	PDBSum Proteopedia
Method	X-RAY DIFFRACTION
Organism
Primary Citation	Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design Rhodes, D.I., Peat, T.S., Vandegraaff, N., Jeevarajah, D., Le, G., Jones, E.D., Smith, J.A., Coates, J.A., Winfield, L.J., Thienthong, N., Newman, J., Lucent, D., Ryan, J.H., Savage, G.P., Francis, C.L., Deadman, J.J. ANTIVIR.CHEM.CHEMOTHER.