PDBsum entry 8oyc

Lyase

PDB id: 8oyc

Contents

Protein chains

460 a.a.

425 a.a.

DNA/RNA

Ligands

SO4

FDA ×2

Waters ×192

PDB id:

8oyc

Name:

Lyase

Title:

Time-resolved sfx structure of the class ii photolyase complexed with a thymine dimer (100 microsecond timpeoint)

Structure:

Deoxyribodipyrimidine photo-lyase. Chain: a, b. Synonym: DNA photolyase. Engineered: yes. Cpd-comprising oligonucleotide. Chain: c, e. Engineered: yes. Counterstrand-oligonucleotide. Chain: d, f.

Source:

Methanosarcina mazei go1. Organism_taxid: 192952. Gene: mm_0852. Expressed in: methanosarcina mazei go1. Expression_system_taxid: 192952. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630

Resolution:

2.50Å R-factor: 0.307 R-free: 0.371

Authors:

T.J.Lane,N.-E.Christou,D.V.M.Melo,V.Apostolopoulou,A.Pateras, A.R.Mashhour,M.Galchenkova,S.Gunther,P.Reinke,V.Kremling, D.Oberthuer,A.Henkel,J.Sprenger,T.E.S.Scheer,E.Lange,O.N.Yefanov, P.Middendorf,J.A.Sellberg,R.Schubert,A.Fadini,C.Cirelli,E.V.Beale, P.Johnson,F.Dworkowski,D.Ozerov,Q.Bertrand,M.Wranik,E.D.Zitter, D.Turk,S.Bajt,H.Chapman,C.Bacellar

Key ref:

T.J.Lane et al. Time-Resolved crystallography captures light-Driven d repair. Science, . PubMed id: 38033070

Date:

03-May-23 Release date: 22-Nov-23

Protein chain

Q8PYK9  (Q8PYK9_METMA) -  Deoxyribodipyrimidine photo-lyase from Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)

Seq: 464 a.a.

Struc: 460 a.a.

Protein chain

Q8PYK9  (Q8PYK9_METMA) -  Deoxyribodipyrimidine photo-lyase from Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)

Seq: 464 a.a.

Struc: 425 a.a.

DNA/RNA chains

A-T-C-G-G-C-T-T-C-G-C-G-C-A 14 bases

T-T-G-C-G-C-G-A-A-G-C-C-G-A 14 bases

C-G-G-C-T-T-C-G-C-G-C-A 12 bases

T-T-G-C-G-C-G-A-A-G-C-C-G 13 bases

Enzyme reactions

• Enzyme class: Chains A, B: E.C.4.1.99.3 - deoxyribodipyrimidine photo-lyase.
• Pathway: EC 4.1.99.3
• Reaction: cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)
• Cofactor: 5,10-methenyltetrahydrofolate; FAD

5,10-methenyltetrahydrofolate FAD (Bound ligand (Het Group name = FDA) corresponds exactly)

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