7QYR | pdb_00007qyr

Crystal structure of RimK from Pseudomonas aeruginosa PAO1

PDB DOI: https://doi.org/10.2210/pdb7QYR/pdb

Classification: LIGASE
Organism(s): Pseudomonas aeruginosa PAO1, synthetic construct
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2022-01-29 Released: 2022-10-05
Deposition Author(s): Thompson, C.M.A., Little, R.H., Stevenson, C.E.M., Lawson, D.M., Malone, J.G.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.232 (Depositor), 0.232 (DCC)
R-Value Work:
0.212 (Depositor), 0.213 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural insights into the mechanism of adaptive ribosomal modification by Pseudomonas RimK.

Thompson, C.M.A., Little, R.H., Stevenson, C.E.M., Lawson, D.M., Malone, J.G.

(2023) Proteins 91: 300-314

PubMed: 36134899 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/prot.26429
Primary Citation Related Structures:
7QYR, 7QYS

PubMed Abstract:
Bacteria are equipped with a diverse set of regulatory tools that allow them to quickly adapt to their environment. The RimK system allows for Pseudomonas spp. to adapt through post-transcriptional regulation by altering the ribosomal subunit RpsF. RimK is found in a wide range of bacteria with a conserved amino acid sequence, however, the genetic context and the role of this protein is highly diverse. By solving and comparing the structures of RimK homologs from two related but functionally divergent systems, we uncovered key structural differences that likely contribute to the different activity levels of each of these homologs. Moreover, we were able to clearly resolve the active site of this protein for the first time, resolving binding of the glutamate substrate. This work advances our understanding of how subtle differences in protein sequence and structure can have profound effects on protein activity, which can in turn result in widespread mechanistic changes.

Organizational Affiliation

Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom.

Macromolecule Content

Total Structure Weight: 338.95 kDa
Atom Count: 17,790
Modeled Residue Count: 2,345
Deposited Residue Count: 2,992
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable alpha-L-glutamate ligase	A, B, C, D, E A, B, C, D, E, F, G, H	314	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: rimK, PA5197 EC: 6.3.2
UniProt
Find proteins for Q9HTZ2 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HTZ2 Go to UniProtKB: Q9HTZ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HTZ2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
poly-glutamate	I [auth K] J [auth L] K [auth M] L [auth N] M [auth O] I [auth K], J [auth L], K [auth M], L [auth N], M [auth O], N [auth P], O [auth Q], P [auth T]	60	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 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 X [auth H] SDF format, chain W [auth G] SDF format, chain V [auth F] SDF format, chain U [auth E] SDF format, chain T [auth D] SDF format, chain S [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth A] MOL2 format, chain X [auth H] MOL2 format, chain W [auth G] MOL2 format, chain V [auth F] MOL2 format, chain U [auth E] MOL2 format, chain T [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth A] mmCIF format, chain X [auth H] mmCIF format, chain W [auth G] mmCIF format, chain V [auth F] mmCIF format, chain U [auth E] mmCIF format, chain T [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth A]	Q [auth A] R [auth B] S [auth C] T [auth D] U [auth E] Q [auth A], R [auth B], S [auth C], T [auth D], U [auth E], V [auth F], W [auth G], X [auth H]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Interactions & Density Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.232 (Depositor), 0.232 (DCC)
R-Value Work: 0.212 (Depositor), 0.213 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.898	α = 90
b = 153.586	β = 102.39
c = 138.539	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-10-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R018154/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BBS/E/J/000PR9797
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BBS/E/J/000PR9790