5ND5

Crystal structure of transketolase from Chlamydomonas reinhardtii in complex with TPP and Mg2+

PDB DOI: https://doi.org/10.2210/pdb5ND5/pdb

Classification: TRANSFERASE
Organism(s): Chlamydomonas reinhardtii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-03-07 Released: 2017-06-07
Deposition Author(s): Fermani, S., Zaffagnini, M., Francia, F., Pasquini, M.
Funding Organization(s): University of Bologna, Alma Mater Studiourum

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.186
R-Value Work: 0.145
R-Value Observed: 0.147

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural basis for the magnesium-dependent activation of transketolase from Chlamydomonas reinhardtii.

Pasquini, M., Fermani, S., Tedesco, D., Sciabolini, C., Crozet, P., Naldi, M., Henri, J., Vothknecht, U., Bertucci, C., Lemaire, S.D., Zaffagnini, M., Francia, F.

(2017) Biochim Biophys Acta 1861: 2132-2145

PubMed: 28552632 Search on PubMed
DOI: https://doi.org/10.1016/j.bbagen.2017.05.021
Primary Citation of Related Structures:
5ND5, 5ND6

PubMed Abstract:
In photosynthetic organisms, transketolase (TK) is involved in the Calvin-Benson cycle and participates to the regeneration of ribulose-5-phosphate. Previous studies demonstrated that TK catalysis is strictly dependent on thiamine pyrophosphate (TPP) and divalent ions such as Mg ²⁺.

Organizational Affiliation

Institut de Biologie Physico-Chimique, UMR8226, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes CNRS, Sorbonne Universités, UPMC, Univ Paris 06, Paris, France.

Macromolecule Content

Total Structure Weight: 151.43 kDa
Atom Count: 10,992
Modelled Residue Count: 1,338
Deposited Residue Count: 1,384
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transketolase	A, B	692	Chlamydomonas reinhardtii	Mutation(s): 0 Gene Names: TRK1, CHLREDRAFT_141319, CHLRE_02g080200v5 EC: 2.2.1.1
UniProt
Find proteins for A8IAN1 (Chlamydomonas reinhardtii) Explore A8IAN1 Go to UniProtKB: A8IAN1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8IAN1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP Query on TPP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]