4GCV | pdb_00004gcv

Structure of a Putative transcription factor (PA1374)from Pseudomonas aeruginosa

PDB DOI: https://doi.org/10.2210/pdb4GCV/pdb

Classification: TRANSCRIPTION
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-07-31 Released: 2013-07-24
Deposition Author(s): Choe, J., Kim, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.287 (Depositor), 0.300 (DCC)
R-Value Work:
0.214 (Depositor), 0.228 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The X-ray crystal structure of PA1374 from Pseudomonas aeruginosa, a putative oxidative-stress sensing transcriptional regulator.

Kim, H., Choe, J.

(2013) Biochem Biophys Res Commun 431: 376-381

PubMed: 23337505 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2013.01.044
Primary Citation Related Structures:
4GCV

PubMed Abstract:
Members of the multiple antibiotic resistance regulator (MarR) family regulate the expression of genes related to antibiotic resistance, oxidative stress, and virulence in bacteria and Archaea. Here, we determined the structure of PA1374 from Pseudomonas aeruginosa at 2.3Å resolution. PA1374 belonged to the MarR family and its structure revealed a tightly bound dimer with each subunit containing a winged helix-turn-helix (wHTH) DNA-binding motif. Conserved arginine residues, Arg55, Arg74, and Arg77, were located in the wHTH region, which might be important to DNA binding. Furthermore, each monomer contained a pocket made of conserved hydrophobic residues. A highly conserved Cys11 located at one end of this pocket may undergo oxidation by organic hydroperoxide molecules, as shown in other MarR family proteins acting as redox-sensing regulators. These results provide insights about the role of PA1374 as a putative oxidative-stress sensing transcriptional regulator.

Organizational Affiliation

Department of Life Science, University of Seoul, Seoul 130-743, Republic of Korea.

Macromolecule Content

Total Structure Weight: 235.97 kDa
Atom Count: 14,604
Modeled Residue Count: 1,717
Deposited Residue Count: 2,016
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcription protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	168	Pseudomonas aeruginosa PAO1	Mutation(s): 2 Gene Names: PA1374
UniProt
Find proteins for Q9I3X0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I3X0 Go to UniProtKB: Q9I3X0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I3X0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain JA [auth K] SDF format, chain P [auth B] SDF format, chain V [auth D] SDF format, chain Z [auth F] MOL2 format, chain JA [auth K] MOL2 format, chain P [auth B] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth F] mmCIF format, chain JA [auth K] mmCIF format, chain P [auth B] mmCIF format, chain V [auth D] mmCIF format, chain Z [auth F]	JA [auth K], P [auth B], V [auth D], Z [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain JA [auth K] Focus chain P [auth B] Focus chain V [auth D] Focus chain Z [auth F] Interactions & Density Focus chain JA [auth K] Focus chain P [auth B] Focus chain V [auth D] Focus chain Z [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain DA [auth H] SDF format, chain FA [auth I] SDF format, chain HA [auth J] SDF format, chain KA [auth K] SDF format, chain MA [auth L] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth C] SDF format, chain W [auth D] MOL2 format, chain BA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain FA [auth I] MOL2 format, chain HA [auth J] MOL2 format, chain KA [auth K] MOL2 format, chain MA [auth L] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] mmCIF format, chain BA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain FA [auth I] mmCIF format, chain HA [auth J] mmCIF format, chain KA [auth K] mmCIF format, chain MA [auth L] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D]	BA [auth G] DA [auth H] FA [auth I] HA [auth J] KA [auth K] BA [auth G], DA [auth H], FA [auth I], HA [auth J], KA [auth K], MA [auth L], N [auth A], Q [auth B], R [auth B], S [auth B], T [auth C], W [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain DA [auth H] Focus chain FA [auth I] Focus chain HA [auth J] Focus chain KA [auth K] Focus chain MA [auth L] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain W [auth D] Interactions & Density Focus chain BA [auth G] Focus chain DA [auth H] Focus chain FA [auth I] Focus chain HA [auth J] Focus chain KA [auth K] Focus chain MA [auth L] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain W [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain CA [auth H] SDF format, chain EA [auth I] SDF format, chain GA [auth J] SDF format, chain IA [auth K] SDF format, chain LA [auth L] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain X [auth E] SDF format, chain Y [auth F] SDF format, chain U [auth D] MOL2 format, chain AA [auth G] MOL2 format, chain CA [auth H] MOL2 format, chain EA [auth I] MOL2 format, chain GA [auth J] MOL2 format, chain IA [auth K] MOL2 format, chain LA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain U [auth D] mmCIF format, chain AA [auth G] mmCIF format, chain CA [auth H] mmCIF format, chain EA [auth I] mmCIF format, chain GA [auth J] mmCIF format, chain IA [auth K] mmCIF format, chain LA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth F] mmCIF format, chain U [auth D]	AA [auth G] CA [auth H] EA [auth I] GA [auth J] IA [auth K] AA [auth G], CA [auth H], EA [auth I], GA [auth J], IA [auth K], LA [auth L], M [auth A], O [auth B], U [auth D], X [auth E], Y [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain CA [auth H] Focus chain EA [auth I] Focus chain GA [auth J] Focus chain IA [auth K] Focus chain LA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain U [auth D] Focus chain X [auth E] Focus chain Y [auth F] Interactions & Density Focus chain AA [auth G] Focus chain CA [auth H] Focus chain EA [auth I] Focus chain GA [auth J] Focus chain IA [auth K] Focus chain LA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain U [auth D] Focus chain X [auth E] Focus chain Y [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.287 (Depositor), 0.300 (DCC)
R-Value Work: 0.214 (Depositor), 0.228 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.897	α = 90
b = 74.448	β = 90.03
c = 230.492	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-07-24

Deposition Author(s):

Choe, J.

Kim, H.

Revision History (Full details and data files)

Version 1.0: 2013-07-24
Type: Initial release
Version 1.1: 2013-07-31
Changes: Data collection
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary