6L7Q

Crystal structure of a hypothetical protein PYCH_01220 derived from Pyrococcus yayanosii

PDB DOI: https://doi.org/10.2210/pdb6L7Q/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Pyrococcus yayanosii CH1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-11-02 Released: 2020-11-04
Deposition Author(s): Jeon, J.-H., Noh, H., Oh, B.-H.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free: 0.205
R-Value Work: 0.192
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of PYCH_01220 from Pyrococcus yayanosii potentially involved in binding nucleic acid.

Noh, H., Jeon, J.H., Kim, Y.G., Oh, B.H.

(2021) Proteins 89: 468-472

PubMed: 33236809 Search on PubMed
DOI: https://doi.org/10.1002/prot.26029
Primary Citation of Related Structures:
6L7Q

PubMed Abstract:
We report the crystal structure of PYCH_01220, a hypothetical protein in Pyrococcus yayanosii CH1. This protein is composed of two domains, named Domain A and Domain B. While Domain B is not significantly homologous to known protein structures, Domain A is structurally analogous to the C-terminal ribonuclease domain of Escherichia coli colicin D. Domain A has a positively charged surface patch rendered by 13 basic residues, eight arginine or lysine residues of which are evolutionarily conserved. Electrophoretic mobility shift assays showed that PYCH_01220 binds to DNA, and charge-inversion mutations on this patch negatively affect the DNA binding, suggesting that the function of PYCH_01220 might involve nucleic acid-binding via the positively charged patch.

Organizational Affiliation

Department of Biological Sciences, KAIST Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.

Macromolecule Content

Total Structure Weight: 17.01 kDa
Atom Count: 1,374
Modelled Residue Count: 145
Deposited Residue Count: 145
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein	A	145	Pyrococcus yayanosii CH1	Mutation(s): 0 Gene Names: PYCH_01220
UniProt
Find proteins for F8AFT0 (Pyrococcus yayanosii (strain CH1 / JCM 16557)) Explore F8AFT0 Go to UniProtKB: F8AFT0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F8AFT0
Sequence Annotations Expand
Reference Sequence