6Z9C
Structure of human POLDIP2, a multifaceted adaptor protein in metabolism and genome stability
Summary for 6Z9C
| Entry DOI | 10.2210/pdb6z9c/pdb |
| Descriptor | Polymerase delta-interacting protein 2, SODIUM ION (3 entities in total) |
| Functional Keywords | poldip2 pdip38 mitochondria nucleus primpol dna polymerase, replication |
| Biological source | Homo sapiens (Human) |
| Total number of polymer chains | 1 |
| Total formula weight | 37043.43 |
| Authors | Kulik, A.A.,Maruszczak, K.,Nabi, N.L.M.,Bingham, R.J.,Cooper, C.D.O. (deposition date: 2020-06-03, release date: 2020-06-17, Last modification date: 2024-01-24) |
| Primary citation | Kulik, A.A.,Maruszczak, K.K.,Thomas, D.C.,Nabi-Aldridge, N.L.A.,Carr, M.,Bingham, R.J.,Cooper, C.D.O. Crystal structure and molecular dynamics of human POLDIP2, a multifaceted adaptor protein in metabolism and genome stability. Protein Sci., 30:1196-1209, 2021 Cited by PubMed Abstract: Polymerase δ-interacting protein 2 (POLDIP2, PDIP38) is a multifaceted, "moonlighting" protein, involved in binding protein partners from many different cellular processes, including mitochondrial metabolism and DNA replication and repair. How POLDIP2 interacts with many different proteins is unknown. Towards this goal, we present the crystal structure of POLDIP2 to 2.8 Å, which exhibited a compact two-domain β-strand-rich globular structure, confirmed by circular dichroism and small angle X-ray scattering approaches. POLDIP2 comprised canonical DUF525 and YccV domains, but with a conserved domain linker packed tightly, resulting in an "extended" YccV module. A central channel was observed, which we hypothesize could influence structural changes potentially mediated by redox conditions, following observation of a modified cysteine residue in the channel. Unstructured regions were rebuilt by ab initio modelling to generate a model of full-length POLDIP2. Molecular dynamics simulations revealed a highly dynamic N-terminal region tethered to the YccV-domain by an extended linker, potentially facilitating interactions with distal binding partners. Models of POLDIP2 complexed with two of its partners, PrimPol and PCNA, indicated that dynamic flexibility of the POLDIP2 N-terminus and loop regions likely mediate protein interactions. PubMed: 33884680DOI: 10.1002/pro.4085 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.8 Å) |
Structure validation
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