7OTJ | pdb_00007otj

Crystal structure of Pif1 helicase from Candida albicans

PDB DOI: https://doi.org/10.2210/pdb7OTJ/pdb
NAKB: 7OTJ

Classification: HYDROLASE
Organism(s): Candida albicans
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2021-06-10 Released: 2021-07-07
Deposition Author(s): Rety, S., Xi, X.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free:
0.242 (Depositor), 0.243 (DCC)
R-Value Work:
0.206 (Depositor), 0.207 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural study of the function of Candida Albicans Pif1.

Lu, K.Y., Xin, B.G., Zhang, T., Liu, N.N., Li, D., Rety, S., Xi, X.G.

(2021) Biochem Biophys Res Commun 567: 190-194

PubMed: 34166917 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2021.06.050
Primary Citation Related Structures:
7OTJ

PubMed Abstract:
Pif1 helicases, conserved in eukaryotes, are involved in maintaining genome stability in both the nucleus and mitochondria. Here, we report the crystal structure of a truncated Candida Albicans Pif1 (CaPif1 ^368-883) in complex with ssDNA and an ATP analog. Our results show that the Q-motif is responsible for identifying adenine bases, and CaPif1 preferentially utilizes ATP/dATP during dsDNA unwinding. Although CaPif1 shares structural similarities with Saccharomyces cerevisiae Pif1, CaPif1 can contact the thymidine bases of DNA by hydrogen bonds, whereas ScPif1 cannot. More importantly, the crosslinking and mutant experiments have demonstrated that the conformational change of domain 2B is necessary for CaPif1 to unwind dsDNA. These findings contribute to further the understanding of the unwinding mechanism of Pif1.

Organizational Affiliation

College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.

Macromolecule Content

Total Structure Weight: 122.33 kDa
Atom Count: 7,347
Modeled Residue Count: 886
Deposited Residue Count: 1,048
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent DNA helicase PIF1	A, B	518	Candida albicans	Mutation(s): 0 EC: 3.6.4.12 (PDB Primary Data), 5.6.2.3 (UniProt)
UniProt
Find proteins for Q59RQ0 (Candida albicans (strain SC5314 / ATCC MYA-2876)) Explore Q59RQ0 Go to UniProtKB: Q59RQ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q59RQ0
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(PTPTPTPTPTPT)-3')	C, D	6	Candida albicans
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain E [auth A] MOL2 format, chain S [auth B] MOL2 format, chain E [auth A] mmCIF format, chain S [auth B] mmCIF format, chain E [auth A]	E [auth A], S [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain S [auth B]
ALF (Subject of Investigation/LOI) Query on ALF Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain F [auth A] MOL2 format, chain T [auth B] MOL2 format, chain F [auth A] mmCIF format, chain T [auth B] mmCIF format, chain F [auth A]	F [auth A], T [auth B]	TETRAFLUOROALUMINATE ION Al F₄ UYOMQIYKOOHAMK-UHFFFAOYSA-J		Interactions Focus chain F [auth A] Focus chain T [auth B] Interactions & Density Focus chain F [auth A] Focus chain T [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A]	O [auth A], P [auth A], Q [auth A], R [auth A], Y [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain Y [auth B] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain Y [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], V [auth B], W [auth B], X [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain G [auth A] MOL2 format, chain U [auth B] MOL2 format, chain G [auth A] mmCIF format, chain U [auth B] mmCIF format, chain G [auth A]	G [auth A], U [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain U [auth B] Interactions & Density Focus chain G [auth A] Focus chain U [auth B]