PDBsum entry 9f12

DNA binding protein

PDB id: 9f12

Contents

Protein chains

95 a.a.

94 a.a.

120 a.a.

109 a.a.

109 a.a.

564 a.a.

DNA/RNA

Metals

_MG

PDB id:

9f12

Name:

DNA binding protein

Title:

Cryoem structure of the f plasmid relaxosome with orit DNA ss-27_-3ds- 2_+143 and trai its te mode, derived from ss-27_-3ds-2_+143-r locally-refined 3.42 a map.

Structure:

T-strand DNA (96-mer). Chain: a. Engineered: yes. R-strand DNA (85-mer). Chain: b. Engineered: yes. Integration host factor subunit alpha. Chain: c. Synonym: ihf-alpha.

Source:

Synthetic: yes. Escherichia coli k-12. Organism_taxid: 83333. Gene: ihfa, hid, hima, b1712, jw1702. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: ihfb, himd, hip, b0912, jw0895. Gene: tray, ecok12f073. Gene: trai, ecok12f104.

Authors:

S.M.Williams,G.Waksman

Key ref:

S.M.Williams et al. (2025). Cryo-Em structure of the relaxosome, A complex essent bacterial mating and the spread of antibiotic resista genes.. Nat commun, 16, 4906. PubMed id: 40425557 DOI: 10.1038/S41467-025-60116-6

Date:

17-Apr-24 Release date: 04-Jun-25

Protein chain

P0A6X7  (IHFA_ECOLI) -  Integration host factor subunit alpha from Escherichia coli (strain K12)

Seq: 99 a.a.

Struc: 95 a.a.

Protein chain

P0A6Y1  (IHFB_ECOLI) -  Integration host factor subunit beta from Escherichia coli (strain K12)

Seq: 94 a.a.

Struc: 94 a.a.

Protein chain

P06627  (TRAY1_ECOLI) -  Relaxosome protein TraY from Escherichia coli (strain K12)

Seq: 131 a.a.

Struc: 120 a.a.

Protein chain

P06627  (TRAY1_ECOLI) -  Relaxosome protein TraY from Escherichia coli (strain K12)

Seq: 131 a.a.

Struc: 109 a.a.

Protein chain

P06627  (TRAY1_ECOLI) -  Relaxosome protein TraY from Escherichia coli (strain K12)

Seq: 131 a.a.

Struc: 109 a.a.

Protein chain

P14565  (TRAI1_ECOLI) -  Multifunctional conjugation protein TraI from Escherichia coli (strain K12)

Seq: 1756 a.a.

Struc: 564 a.a.*

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

DNA/RNA chains

T-T-T-A-A-A-T-A-T-C-A-T-A-A-A-G-A-G-A-G-T-A-A-G-A-G-A-A-A-C-T-A-A-T-T-T-T-T-C- 96 bases

G-C-A-A-A-A-A-C-A-A-G-T-T-T-T-T-G-C-T-G-A-T-T-T-T-T-C-T-T-T-A-T-A-A-A-T-A-G-A- 85 bases

Enzyme reactions

• Enzyme class 2: Chain H: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 3: Chain H: E.C.5.6.2.1 - Dna topoisomerase.

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