7ANU | pdb_00007anu

Crystal structure of Pyrococcus abyssi Pbp11

PDB DOI: https://doi.org/10.2210/pdb7ANU/pdb

Classification: PROTEIN BINDING
Organism(s): Pyrococcus abyssi GE5
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-10-12 Released: 2021-11-03
Deposition Author(s): Hogrel, G., Girard, E., Franzetti, B.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.222 (Depositor), 0.226 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Characterization of a small tRNA-binding protein that interacts with the archaeal proteasome complex.

Hogrel, G., Marino-Puertas, L., Laurent, S., Ibrahim, Z., Coves, J., Girard, E., Gabel, F., Fenel, D., Daugeron, M.C., Clouet-d'Orval, B., Basta, T., Flament, D., Franzetti, B.

(2022) Mol Microbiol 118: 16-29

PubMed: 35615908 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1111/mmi.14948
Primary Citation Related Structures:
7ANU

PubMed Abstract:
The proteasome system allows the elimination of functional or structurally impaired proteins. This includes the degradation of nascent peptides. In Archaea, how the proteasome complex interacts with the translational machinery remains to be described. Here, we characterized a small orphan protein, Q9UZY3 (UniProt ID), conserved in Thermococcales. The protein was identified in native pull-down experiments using the proteasome regulatory complex (proteasome-activating nucleotidase [PAN]) as bait. X-ray crystallography and small-angle X-ray scattering experiments revealed that the protein is monomeric and adopts a β-barrel core structure with an oligonucleotide/oligosaccharide-binding (OB)-fold, typically found in translation elongation factors. Mobility shift experiment showed that Q9UZY3 displays transfer ribonucleic acid (tRNA)-binding properties. Pull-downs, co-immunoprecipitation and isothermal titration calorimetry (ITC) studies revealed that Q9UZY3 interacts in vitro with PAN. Native pull-downs and proteomic analysis using different versions of Q9UZY3 showed that the protein interacts with the assembled PAN-20S proteasome machinery in Pyrococcus abyssi (Pa) cellular extracts. The protein was therefore named Pbp11, for Proteasome-Binding Protein of 11 kDa. Interestingly, the interaction network of Pbp11 also includes ribosomal proteins, tRNA-processing enzymes and exosome subunits dependent on Pbp11's N-terminal domain that was found to be essential for tRNA binding. Together these data suggest that Pbp11 participates in an interface between the proteasome and the translational machinery.

Organizational Affiliation

CNRS, CEA, IBS, Univ Grenoble Alpes, Grenoble, France.

Macromolecule Content

Total Structure Weight: 21.47 kDa
Atom Count: 1,511
Modeled Residue Count: 174
Deposited Residue Count: 184
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pbp11 protein	A, B	92	Pyrococcus abyssi GE5	Mutation(s): 0 Gene Names: PAB1698
UniProt
Find proteins for Q9UZY3 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9UZY3 Go to UniProtKB: Q9UZY3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UZY3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A]	H [auth A], I [auth B], L [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain L [auth B]