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Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with DNA

X-ray diffraction
2.4Å resolution
PDB entry 2r9l coloured by chain, front view.
PDB entry 2r9l coloured by chain, side view.
PDB entry 2r9l coloured by chain, top view.
Source organisms:
Assembly composition:
hetero trimer (preferred)
Entry contents: 1 distinct polypeptide molecule
3 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Multifunctional non-homologous end joining DNA repair protein LigD and DNA
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Multimeric state: hetero trimer
Accessible surface area: 14958.36 Å2
Buried surface area: 3157.63 Å2
Dissociation area: 830.44 Å2
Dissociation energy (ΔGdiss): 6.08 kcal/mol
Dissociation entropy (TΔSdiss): 10.71 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-218919
Assembly 2
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Assembly Name: Multifunctional non-homologous end joining DNA repair protein LigD and DNA
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Multimeric state: hetero trimer
Accessible surface area: 15265.82 Å2
Buried surface area: 2618.07 Å2
Dissociation area: 518.91 Å2
Dissociation energy (ΔGdiss): 10.05 kcal/mol
Dissociation entropy (TΔSdiss): 7.92 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-218920

Macromolecules

Multifunctional non-homologous end joining DNA repair protein LigD
Chains: A, B
Length: 303 amino acids
Theoretical weight: 32.83 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P9WNV3 (Residues: 1-300; Coverage: 40%)
Gene names: MTCY08D9.01c, MTCY10D7.36c, Rv0938, ligD
Pfam: LigD, primase-polymerase domain
InterPro:
CATH: Alpha-Beta Plaits
Multifunctional non-homologous end joining DNA repair protein LigD in PDB entry 2r9l, assembly 1, front view.
Multifunctional non-homologous end joining DNA repair protein LigD in PDB entry 2r9l, assembly 1, side view.
Multifunctional non-homologous end joining DNA repair protein LigD in PDB entry 2r9l, assembly 1, top view.
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DNA chains C, E
Name: DNA (5'-D(P*DGP*DCP*DGP*DGP*DC)-3')
Representative chains: C, E
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 5 nucleotides
Theoretical weight: 1.52 KDa
DNA (5'-D(P*DGP*DCP*DGP*DGP*DC)-3') in PDB entry 2r9l, assembly 1, front view.
DNA (5'-D(P*DGP*DCP*DGP*DGP*DC)-3') in PDB entry 2r9l, assembly 1, side view.
DNA (5'-D(P*DGP*DCP*DGP*DGP*DC)-3') in PDB entry 2r9l, assembly 1, top view.
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DNA chain D
Name: DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DA)-3')
Representative chains: D
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 11 nucleotides
Theoretical weight: 3.33 KDa
DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DA)-3') in PDB entry 2r9l, assembly 1, front view.
DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DA)-3') in PDB entry 2r9l, assembly 1, side view.
DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DA)-3') in PDB entry 2r9l, assembly 1, top view.
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DNA chain F
Name: DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DAP*DCP*DG)-3')
Representative chains: F
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DAP*DCP*DG)-3') in PDB entry 2r9l, assembly 2, front view.
DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DAP*DCP*DG)-3') in PDB entry 2r9l, assembly 2, side view.
DNA (5'-D(*DGP*DCP*DCP*DGP*DCP*DAP*DAP*DCP*DGP*DCP*DAP*DCP*DG)-3') in PDB entry 2r9l, assembly 2, top view.
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