4X3F | pdb_00004x3f

Crystal structure of the intracellular domain of the M. tuberculosis Ser/Thr kinase PknA

PDB DOI: https://doi.org/10.2210/pdb4X3F/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-11-28 Released: 2015-01-21
Deposition Author(s): Wagner, T., Wehenkel, A., Alzari, P.M., Bellinzoni, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.243 (Depositor), 0.242 (DCC)
R-Value Work:
0.219 (Depositor), 0.219 (DCC)
R-Value Observed:
0.220 (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

The crystal structure of the catalytic domain of the ser/thr kinase PknA from M. tuberculosis shows an Src-like autoinhibited conformation.

Wagner, T., Alexandre, M., Duran, R., Barilone, N., Wehenkel, A., Alzari, P.M., Bellinzoni, M.

(2015) Proteins 83: 982-988

PubMed: 25586004 Search on PubMed
DOI: https://doi.org/10.1002/prot.24754
Primary Citation Related Structures:
4X3F

PubMed Abstract:
Signal transduction mediated by Ser/Thr phosphorylation in Mycobacterium tuberculosis has been intensively studied in the last years, as its genome harbors eleven genes coding for eukaryotic-like Ser/Thr kinases. Here we describe the crystal structure and the autophosphorylation sites of the catalytic domain of PknA, one of two protein kinases essential for pathogen's survival. The structure of the ligand-free kinase domain shows an auto-inhibited conformation similar to that observed in human Tyr kinases of the Src-family. These results reinforce the high conservation of structural hallmarks and regulation mechanisms between prokaryotic and eukaryotic protein kinases.

Organizational Affiliation

Institut Pasteur, Unité De Microbiologie Structurale, Paris, 75724, France; CNRS UMR 3528, Paris, 75724, France; Université Paris Diderot, Sorbonne Paris Cité, Microbiologie Structurale, Paris, 75724, France.

Macromolecule Content

Total Structure Weight: 107.81 kDa
Atom Count: 6,027
Modeled Residue Count: 831
Deposited Residue Count: 1,011
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PknA	A	337	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: pknA, Rv0015c, MTCY10H4.15c EC: 2.7.11.1
UniProt
Find proteins for P9WI83 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WI83 Go to UniProtKB: P9WI83
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WI83
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PknA	B	337	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: pknA, Rv0015c, MTCY10H4.15c EC: 2.7.11.1
UniProt
Find proteins for P9WI83 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WI83 Go to UniProtKB: P9WI83
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WI83
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PknA	C	337	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: pknA, Rv0015c, MTCY10H4.15c EC: 2.7.11.1
UniProt
Find proteins for P9WI83 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WI83 Go to UniProtKB: P9WI83
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WI83
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER
TPO Query on TPO	A	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.243 (Depositor), 0.242 (DCC)
R-Value Work: 0.219 (Depositor), 0.219 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.31	α = 90
b = 150.18	β = 96.98
c = 96.54	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-01-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-01-21
Type: Initial release
Version 1.1: 2015-04-22
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary