Brand  (β version)

PDB ID: 3BXS

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Ligands
Code Name Style Show Link
DRS (9s,12s)-9-(1-methylethyl)-7,10-dioxo-2-oxa-8,11-diazabicyclo[12.2.2]octadeca-1(16),14,17-triene-12-carboxylic acid PoSSuM
SO4 Sulfate ion PoSSuM
Non-standard Residues
Code Name Show
ABA Alpha-aminobutyric acid
Glycosylation
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Modification
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Structure summary

Code : 3BXS   PDBj   RCSB PDB   PDBe
Header : HYDROLASE
Title : Crystal Structures Of Highly Constrained Substrate And Hydrolysis Products Bound To HIV-1 Protease. Implications For Catalytic Mechanism
Release Data : 2008-03-25
Compound :
mol_id molecule chains synonym
1 Protease A,B Retropepsin, PR
ec: 3.4.23.16
fragment: UNP residues 491-589
mutation: Q7K, L33I, C67(ABA), C95(ABA), Q107K, L133I, C167(ABA), C195(ABA)
Source :
mol_id organism_scientific
1
synthetic: yes
other_details: Chemically synthesized protein corresponding to the protease from the HIV1
Authors : Tyndall, J.D., Pattenden, L.K., Reid, R.C., Hu, S.H., Alewood, D., Alewood, P.F., Walsh, T., Fairlie, D.P., Martin, J.L.
Keywords : HIV protease, HIVPR, substrate, product, AIDS, Aspartyl protease, Capsid maturation, Core protein, Cytoplasm, DNA integration, DNA recombination, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Lipoprotein, Magnesium, Membrane, Metal-binding, Multifunctional enzyme, Myristate, Nuclease, Nucleotidyltransferase, Nucleus, Phosphoprotein, RNA-binding, RNA-directed DNA polymerase, Transferase, Viral nucleoprotein, Virion, Zinc, Zinc-finger
Exp. method : X-RAY DIFFRACTION ( 1.600 Å )
Citation :

Crystal Structures of Highly Constrained Substrate and Hydrolysis Products Bound to HIV-1 Protease. Implications for the Catalytic Mechanism

Tyndall, J.D.,Pattenden, L.K.,Reid, R.C.  et al.
(2008)  Biochemistry  47 : 3736 - 3744

PubMed: 18311928
DOI: 10.1021/bi7023157

Molecular recognition of macrocyclic peptidomimetic inhibitors by HIV-1 protease

Martin, J.L.,Begun, J.,Schindeler, A.  et al.
(1999)  Biochemistry  38 : 7978 - 7988

PubMed: 10387041
DOI: 10.1021/bi990174x

Reaction

Chain : A, B
UniProt : P03369 (POL_HV1A2)
Reaction: EC: Evidence:
Physiological Direction:
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro. 3.4.23.16 PROSITE-ProRule:PRU00275
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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. 3.1.26.13 ECO:0000250
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3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. 3.1.13.2 ECO:0000250
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 2.7.7.49 PROSITE-ProRule:PRU00405
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 2.7.7.7 PROSITE-ProRule:PRU00405
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Cofactor: Evidence: Note:
Mg(2+) ECO:0000250
Binds 2 magnesium ions for reverse transcriptase polymerase activity.
Mg(2+) ECO:0000250
Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding.
Mg(2+) ECO:0000250
Magnesium ions are required for integrase activity. Binds at least 1, maybe 2 magnesium ions.