2J80 | pdb_00002j80

Structure of Citrate-bound Periplasmic Domain of Sensor Histidine Kinase CitA

PDB DOI: https://doi.org/10.2210/pdb2J80/pdb

Classification: TRANSFERASE
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-10-18 Released: 2007-10-23
Deposition Author(s): Sevvana, M., Vijayan, V., Zweckstetter, M., Reinelt, S., Madden, D.R., Sheldrick, G.M., Bott, M., Griesinger, C., Becker, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.217 (Depositor)
R-Value Work:
0.193 (Depositor), 0.186 (DCC)
R-Value Observed:
0.194 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

A Ligand-Induced Switch in the Periplasmic Domain of Sensor Histidine Kinase Cita.

Sevvana, M., Vijayan, V., Zweckstetter, M., Reinelt, S., Madden, D.R., Herbst-Irmer, R., Sheldrick, G.M., Bott, M., Griesinger, C., Becker, S.

(2008) J Mol Biology 377: 512

PubMed: 18258261 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2008.01.024
Primary Citation Related Structures:
2J80, 2V9A

PubMed Abstract:
Sensor histidine kinases of two-component signal-transduction systems are essential for bacteria to adapt to variable environmental conditions. However, despite their prevalence, it is not well understood how extracellular signals such as ligand binding regulate the activity of these sensor kinases. CitA is the sensor histidine kinase in Klebsiella pneumoniae that regulates the transport and anaerobic metabolism of citrate in response to its extracellular concentration. We report here the X-ray structures of the periplasmic sensor domain of CitA in the citrate-free and citrate-bound states. A comparison of the two structures shows that ligand binding causes a considerable contraction of the sensor domain. This contraction may represent the molecular switch that activates transmembrane signaling in the receptor.

Organizational Affiliation

Department of Structural Chemistry, University of Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany.

Macromolecule Content

Total Structure Weight: 30.56 kDa
Atom Count: 2,136
Modeled Residue Count: 253
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SENSOR KINASE CITA	A, B	135	Klebsiella pneumoniae	Mutation(s): 0 EC: 2.7.13.3
UniProt
Find proteins for P52687 (Klebsiella pneumoniae) Explore P52687 Go to UniProtKB: P52687
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52687
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	F [auth A], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.217 (Depositor)
R-Value Work: 0.193 (Depositor), 0.186 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.21	α = 90
b = 54.79	β = 90
c = 116.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXCD	phasing
SHELXE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-10-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-10-23
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-03-06
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.4: 2019-05-08
Changes: Data collection, Experimental preparation
Version 1.5: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Other, Structure summary