PDBsum entry 6t8h

Replication

PDB id: 6t8h

Contents

Protein chains

246 a.a.

420 a.a.

1188 a.a.

DNA/RNA

Metals

_ZN ×4

_FE

PDB id:

6t8h

Name:

Replication

Title:

Cryo-em structure of the DNA-bound pold-pcna processive complex from p. Abyssi

Structure:

DNA polymerase sliding clamp. Chain: e, c, d. Synonym: proliferating cell nuclear antigen homolog,pcna. Engineered: yes. DNA polymerase ii small subunit. Chain: a. Synonym: pol ii,exodeoxyribonuclease small subunit. Engineered: yes. Mutation: yes.

Source:

Pyrococcus abyssi (strain ge5 / orsay). Organism_taxid: 272844. Strain: ge5 / orsay. Gene: pcn, pyrab13790, pab1465. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: polb, pyrab01210, pab2266. Pyrococcus abyssi. Organism_taxid: 29292.

Authors:

C.Madru,P.Raia,I.Hugonneau Beaufet,G.Pehau-Arnaudet,P.England, E.Lindhal,M.Delarue,M.Carroni,L.Sauguet

Date:

24-Oct-19 Release date: 04-Mar-20

Protein chains

Q9UYX8  (PCNA_PYRAB) -  DNA polymerase sliding clamp from Pyrococcus abyssi (strain GE5 / Orsay)

Seq: 249 a.a.

Struc: 246 a.a.

Protein chain

Q9V2F3  (DP2S_PYRAB) -  DNA polymerase II small subunit from Pyrococcus abyssi (strain GE5 / Orsay)

Seq: 619 a.a.

Struc: 420 a.a.*

Protein chain

Q9V2F4  (DP2L_PYRAB) -  DNA polymerase II large subunit from Pyrococcus abyssi (strain GE5 / Orsay)

Seq: 1455 a.a.

Struc: 1188 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

C-G-C-C-G-G-G-C-C-G-A-G-C-C-G-T-G 17 bases

C-A-C-G-G-C-T-C-G-G-C-C-C-G-G-C-G 17 bases

Enzyme reactions

• Enzyme class 1: 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 2: Chains A, B: E.C.3.1.11.1 - exodeoxyribonuclease I.
• Reaction: Degradation of single-stranded DNA. It acts progressively in a 3'- to 5'-direction, releasing nucleoside 5'-phosphates.

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