PDBsum entry 6s1v

Hydrolase

PDB id: 6s1v

Contents

Protein chains

103 a.a.

105 a.a.

Ligands

PRO-0A1-VAL-PSA-ALA-MET-THR

Waters ×163

PDB id:

6s1v

Name:

Hydrolase

Title:

Crystal structure of dimeric m-pmv protease d26n mutant in complex with inhibitor

Structure:

Gag-pro-pol polyprotein. Chain: a, b. Synonym: pr180. Ec: 3.6.1.23,3.4.23.-,2.7.7.49,2.7.7.7,3.1.26.4,2.7.7.-,3.1.-.-. Engineered: yes. Mutation: yes. Other_details: gaps in the sequence indicate residues that were not modeled because of poor electron density. Pro-0a1-val-psa-ala-met-thr.

Source:

Mason-pfizer monkey virus. Mpmv. Organism_taxid: 11855. Gene: gag-pro-pol. Expressed in: escherichia coli 'bl21-gold(de3)plyss ag'. Expression_system_taxid: 866768. Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Resolution:

1.64Å R-factor: 0.180 R-free: 0.220

Authors:

S.Wosicki,M.Gilski,M.Jaskolski,H.Zabranska,I.Pichova

Key ref:

S.Wosicki et al. (2019). Comparison of a retroviral protease in monomeric and dimeric states. Acta Crystallogr D Struct Biol, 75, 904-917. PubMed id: 31588922 DOI: 10.1107/S2059798319011355

Date:

19-Jun-19 Release date: 16-Oct-19

Protein chain

P07572  (POL_MPMV) -  Gag-Pro-Pol polyprotein from Mason-Pfizer monkey virus

Seq: 1771 a.a.

Struc: 103 a.a.*

Protein chain

P07572  (POL_MPMV) -  Gag-Pro-Pol polyprotein from Mason-Pfizer monkey virus

Seq: 1771 a.a.

Struc: 105 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.2.7.7.- - ?????
• Enzyme class 2: Chains A, B: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: Chains A, B: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: Chains A, B: E.C.3.1.-.-
• Enzyme class 5: Chains A, B: E.C.3.1.26.4 - ribonuclease H.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.
• Enzyme class 6: Chains A, B: E.C.3.4.23.- - ?????
• Enzyme class 7: Chains A, B: E.C.3.6.1.23 - dUTP diphosphatase.
• Reaction: dUTP + H2O = dUMP + diphosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S2059798319011355

Acta Crystallogr D Struct Biol 75:904-917 (2019)

PubMed id: 31588922

Comparison of a retroviral protease in monomeric and dimeric states.

S.Wosicki, M.Gilski, H.Zabranska, I.Pichova, M.Jaskolski.

ABSTRACT

Retroviral proteases (RPs) are of high interest owing to their crucial role in the maturation process of retroviral particles. RPs are obligatory homodimers, with a pepsin-like active site built around two aspartates (in DTG triads) that activate a water molecule, as the nucleophile, under two flap loops. Mason-Pfizer monkey virus (M-PMV) is unique among retroviruses as its protease is also stable in the monomeric form, as confirmed by an existing crystal structure of a 13 kDa variant of the protein (M-PMV PR) and its previous biochemical characterization. In the present work, two mutants of M-PMV PR, D26N and C7A/D26N/C106A, were crystallized in complex with a peptidomimetic inhibitor and one mutant (D26N) was crystallized without the inhibitor. The crystal structures were solved at resolutions of 1.6, 1.9 and 2.0 Å, respectively. At variance with the previous study, all of the new structures have the canonical dimeric form of retroviral proteases. The protomers within a dimer differ mainly in the flap-loop region, with the most extreme case observed in the apo structure, in which one flap loop is well defined while the other flap loop is not defined by electron density. The presence of the inhibitor molecules in the complex structures was assessed using polder maps, but some details of their conformations remain ambiguous. In all of the presented structures the active site contains a water molecule buried deeply between the Asn26-Thr27-Gly28 triads of the protomers. Such a water molecule is completely unique not only in retropepsins but also in aspartic proteases in general. The C7A and C106A mutations do not influence the conformation of the protein. The Cys106 residue is properly placed at the homodimer interface area for a disulfide cross-link, but the reducing conditions of the crystallization experiment prevented S-S bond formation. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:S2059798319011355.