2IHM

Polymerase mu in ternary complex with gapped 11mer DNA duplex and bound incoming nucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

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This is version 1.4 of the entry. See complete history


Literature

Structural insight into the substrate specificity of DNA Polymerase mu.

Moon, A.F.Garcia-Diaz, M.Bebenek, K.Davis, B.J.Zhong, X.Ramsden, D.A.Kunkel, T.A.Pedersen, L.C.

(2007) Nat Struct Mol Biol 14: 45-53

  • DOI: 10.1038/nsmb1180
  • Primary Citation of Related Structures:  
    2IHM

  • PubMed Abstract: 
  • DNA polymerase mu (Pol mu) is a family X enzyme with unique substrate specificity that contributes to its specialized role in nonhomologous DNA end joining (NHEJ). To investigate Pol mu's unusual substrate specificity, we describe the 2.4 A crystal structure of the polymerase domain of murine Pol mu bound to gapped DNA with a correct dNTP at the active site ...

    DNA polymerase mu (Pol mu) is a family X enzyme with unique substrate specificity that contributes to its specialized role in nonhomologous DNA end joining (NHEJ). To investigate Pol mu's unusual substrate specificity, we describe the 2.4 A crystal structure of the polymerase domain of murine Pol mu bound to gapped DNA with a correct dNTP at the active site. This structure reveals substrate interactions with side chains in Pol mu that differ from other family X members. For example, a single amino acid substitution, H329A, has little effect on template-dependent synthesis by Pol mu from a paired primer terminus, but it reduces both template-independent and template-dependent synthesis during NHEJ of intermediates whose 3' ends lack complementary template strand nucleotides. These results provide insight into the substrate specificity and differing functions of four closely related mammalian family X DNA polymerases.


    Organizational Affiliation

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences (National Institutes of Health, US Department of Health and Human Services), 111 T.W. Alexander Drive, MD F3-09, Research Triangle Park, North Carolina 27709, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase muG [auth A],
H [auth B]
360Mus musculusMutation(s): 0 
Gene Names: Polmpolmu
EC: 2.7.7.7
UniProt
Find proteins for Q9JIW4 (Mus musculus)
Explore Q9JIW4 
Go to UniProtKB:  Q9JIW4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JIW4
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3'A [auth T],
D [auth U]
11N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*CP*AP*GP*TP*AP*T)-3'B [auth P],
E [auth Q]
6N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(P*GP*CP*CP*G)-3'C [auth D],
F [auth E]
4N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.028α = 90
b = 96.085β = 106.55
c = 73.09γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
CNSrefinement
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2018-01-24
    Changes: Structure summary