5XEX | pdb_00005xex

Crystal structure of S.aureus PNPase catalytic domain

PDB DOI: https://doi.org/10.2210/pdb5XEX/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus NCTC 8325
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2017-04-06 Released: 2017-10-18
Deposition Author(s): Wang, X., Zhang, X., Zang, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.249 (Depositor), 0.243 (DCC)
R-Value Work:
0.223 (Depositor), 0.223 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Enolase binds to RnpA in competition with PNPase in Staphylococcus aureus

Wang, X., Wang, C., Wu, M., Tian, T., Cheng, T., Zhang, X., Zang, J.

(2017) FEBS Lett 591: 3523-3535

PubMed: 28960276 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.12859
Primary Citation Related Structures:
5XEX

PubMed Abstract:
The RNA degradosome of the pathogen Staphylococcus aureus regulates the metabolism of RNA, the expression of virulence factors, and the formation of biofilms. It is composed of the RNases J1/J2, RNase Y, CshA, PNPase, Enolase, Pfk, and a newly identified component, RnpA. However, the function and new partners of RnpA in RNA degradosome remain unknown. Here, we identified PNPase and Enolase as two novel partners for RnpA. Further studies revealed that Enolase interacts with RnpA in competition with PNPase. Enzymatic assays showed that RnpA increases Enolase activity but has no effect on PNPase. These findings provide more information about the functional relationship between RnpA and RNA degradosome.

Organizational Affiliation

Hefei National Laboratory for Physical Sciences at Microscale CAS Center for Excellence in Biomacromolecules, Collaborative Innovation Center of Chemistry for Life Sciences, and School of Life Sciences, University of Science and Technology of China, Hefei, China.

Macromolecule Content

Total Structure Weight: 375.25 kDa
Atom Count: 24,313
Modeled Residue Count: 3,071
Deposited Residue Count: 3,354
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyribonucleotide nucleotidyltransferase	A, B, C, D, E A, B, C, D, E, F	559	Staphylococcus aureus subsp. aureus NCTC 8325	Mutation(s): 0 Gene Names: pnp, pnpA, SAOUHSC_01251 EC: 2.7.7.8
UniProt
Find proteins for Q2FZ20 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FZ20 Go to UniProtKB: Q2FZ20
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2FZ20
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PPV Query on PPV Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain X [auth F] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain U [auth E] mmCIF format, chain X [auth F]	I [auth A] L [auth B] O [auth C] R [auth D] U [auth E] I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	PYROPHOSPHATE H₄ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain S [auth E] SDF format, chain V [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] MOL2 format, chain V [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain S [auth E] mmCIF format, chain V [auth F]	G [auth A] J [auth B] M [auth C] P [auth D] S [auth E] G [auth A], J [auth B], M [auth C], P [auth D], S [auth E], V [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain T [auth E] SDF format, chain W [auth F] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F]	H [auth A] K [auth B] N [auth C] Q [auth D] T [auth E] H [auth A], K [auth B], N [auth C], Q [auth D], T [auth E], W [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain W [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.249 (Depositor), 0.243 (DCC)
R-Value Work: 0.223 (Depositor), 0.223 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.699	α = 98.22
b = 93.773	β = 95.34
c = 130.242	γ = 120.01

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-10-18

Deposition Author(s):

Wang, X.

Zhang, X.

Zang, J.

Revision History (Full details and data files)

Version 1.0: 2017-10-18
Type: Initial release
Version 1.1: 2017-11-29
Changes: Database references
Version 1.2: 2018-02-07
Changes: Database references
Version 1.3: 2023-11-22
Changes: Data collection, Database references, Refinement description

5XEX | pdb_00005xex

Crystal structure of S.aureus PNPase catalytic domain

Literature

Enolase binds to RnpA in competition with PNPase in Staphylococcus aureus

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand