5XRV

Crystal Structure of Transketolase in complex with TPP_V and fructose-6-phosphate from Pichia Stipitis

PDB DOI: https://doi.org/10.2210/pdb5XRV/pdb

Classification: TRANSFERASE
Organism(s): Scheffersomyces stipitis CBS 6054
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2017-06-09 Released: 2018-06-13
Deposition Author(s): Li, T.L., Hsu, N.S., Wang, Y.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.138
R-Value Work: 0.121
R-Value Observed: 0.122

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Evidence of Diradicals Involved in the Yeast Transketolase Catalyzed Keto-Transferring Reactions.

Hsu, N.S., Wang, Y.L., Lin, K.H., Chang, C.F., Ke, S.C., Lyu, S.Y., Hsu, L.J., Li, Y.S., Chen, S.C., Wang, K.C., Li, T.L.

(2018) Chembiochem 19: 2395-2402

PubMed: 30155962 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/cbic.201800378
Primary Citation of Related Structures:
5XPS, 5XQA, 5XQK, 5XRV, 5XT0, 5XT4, 5XTX, 5XU2, 5XU9

PubMed Abstract:
Transketolase (TK) catalyzes a reversible transfer of a two-carbon (C ₂ ) unit between phosphoketose donors and phosphoaldose acceptors, for which the group-transfer reaction that follows a one- or two-electron mechanism and the force that breaks the C2"-C3" bond of the ketose donors remain unresolved. Herein, we report ultrahigh-resolution crystal structures of a TK (TKps) from Pichia stipitis in previously undiscovered intermediate states and support a diradical mechanism for a reversible group-transfer reaction. In conjunction with MS, NMR spectroscopy, EPR and computational analyses, it is concluded that the enzyme-catalyzed non-Kekulé diradical cofactor brings about the C2"-C3" bond cleavage/formation for the C ₂ -unit transfer reaction, for which suppression of activation energy and activation and destabilization of enzymatic intermediates are facilitated.

Organizational Affiliation

Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.

Macromolecule Content

Total Structure Weight: 76.84 kDa
Atom Count: 6,174
Modelled Residue Count: 675
Deposited Residue Count: 697
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	697	Scheffersomyces stipitis CBS 6054	Mutation(s): 0 Gene Names: TKT, TKT1, PICST_67105 EC: 2.2.1.1
UniProt
Find proteins for P34736 (Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545)) Go to UniProtKB: P34736
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8EF Query on 8EF Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-[(5S)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methylidene-1,3-thiazolidin-5-yl]ethyl phosphono hydrogen phosphate C₁₂ H₂₀ N₄ O₇ P₂ S YBJKPSYOFQHZDJ-NSHDSACASA-N		Interactions Focus chain D [auth A]
TPP Query on TPP Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain K [auth A]
F6R Query on F6R Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FRUCTOSE -6-PHOSPHATE C₆ H₁₃ O₉ P GSXOAOHZAIYLCY-HSUXUTPPSA-N		Interactions Focus chain C [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.138
R-Value Work: 0.121
R-Value Observed: 0.122
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.869	α = 90
b = 183.423	β = 90
c = 98.841	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-06-13

Deposition Author(s):

Li, T.L.

Hsu, N.S.

Wang, Y.L.

Revision History (Full details and data files)

Version 1.0: 2018-06-13
Type: Initial release
Version 1.1: 2018-12-19
Changes: Data collection, Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description