3UPB | pdb_00003upb

1.5 Angstrom Resolution Crystal Structure of Transaldolase from Francisella tularensis in Covalent Complex with Arabinose-5-Phosphate

PDB DOI: https://doi.org/10.2210/pdb3UPB/pdb

Classification: TRANSFERASE
Organism(s): Francisella tularensis subsp. tularensis
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-11-17 Released: 2011-11-30
Deposition Author(s): Light, S.H., Minasov, G., Shuvalova, L., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.175 (Depositor), 0.180 (DCC)
R-Value Work:
0.151 (Depositor), 0.160 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Arabinose 5-phosphate covalently inhibits transaldolase.

Light, S.H., Anderson, W.F.

(2014) J Struct Funct Genomics 15: 41-44

PubMed: 24510200 Search on PubMed
DOI: https://doi.org/10.1007/s10969-014-9174-1
Primary Citation of Related Structures:
3UPB

PubMed Abstract:
Arabinose 5-phosphate (A5P) is the aldopentose version of the ketohexose fructose 6-phosphate (F6P), having identical stereochemistry but lacking atoms corresponding to the 1-carbon and 1-hydroxyl. Despite structural similarity and conservation of the reactive portion of F6P, F6P acts as a substrate whereas A5P is reported to be an inhibitor of transaldolase. To address the lack of A5P reactivity we determined a crystal structure of the Francisella tularensis transaldolase in complex with A5P. This structure reveals that like F6P, A5P forms a covalent Schiff base with active site Lys135. Unlike F6P, A5P binding fails to displace an ordered active site water molecule. Retaining this water necessitates conformational changes at the A5P-protein linkage that possibly hinder reactivity. The findings presented here show the basis of A5P inhibition and suggest an unusual mechanism of competitive, reversible-covalent transaldolase regulation.

Organizational Affiliation

Center for Structural Genomics of Infectious Diseases, Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.

Macromolecule Content

Total Structure Weight: 78.21 kDa
Atom Count: 5,864
Modeled Residue Count: 620
Deposited Residue Count: 690
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transaldolase	A, B	345	Francisella tularensis subsp. tularensis	Mutation(s): 0 Gene Names: FTT_1093c, talA EC: 2.2.1.2
UniProt
Find proteins for Q5NFX0 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NFX0 Go to UniProtKB: Q5NFX0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5NFX0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G 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]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
A5P Query on A5P 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]	ARABINOSE-5-PHOSPHATE C₅ H₁₃ O₈ P VJDOAZKNBQCAGE-WDCZJNDASA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
PEG Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.175 (Depositor), 0.180 (DCC)
R-Value Work: 0.151 (Depositor), 0.160 (DCC)
R-Value Observed: 0.152 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33upb

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.045	α = 90
b = 86.197	β = 90
c = 140.547	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-11-30

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-11-30
Type: Initial release
Version 1.1: 2014-03-05
Changes: Database references
Version 1.2: 2014-04-09
Changes: Database references
Version 1.3: 2017-11-08
Changes: Refinement description
Version 1.4: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-11-06
Changes: Structure summary