6Y0K | pdb_00006y0k

Sulfite oxidase from Thermus thermophilus with coordinated phosphate

PDB DOI: https://doi.org/10.2210/pdb6Y0K/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2020-02-08 Released: 2020-08-05
Deposition Author(s): Djeghader, A., Soulimane, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.191 (Depositor), 0.196 (DCC)
R-Value Work:
0.166 (Depositor), 0.177 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural evidence for a reaction intermediate mimic in the active site of a sulfite dehydrogenase.

Djeghader, A., Rossotti, M., Abdulkarim, S., Biaso, F., Gerbaud, G., Nitschke, W., Schoepp-Cothenet, B., Soulimane, T., Grimaldi, S.

(2020) Chem Commun (Camb) 56: 9850-9853

PubMed: 32716419 Search on PubMed
DOI: https://doi.org/10.1039/d0cc03634j
Primary Citation Related Structures:
6Y0K

PubMed Abstract:
By combining X-ray crystallography, electron paramagnetic resonance techniques and density functional theory-based modelling, we provide evidence for a direct coordination of the product analogue, phosphate, to the molybdenum active site of a sulfite dehydrogenase. This interaction is mimicking the still experimentally uncharacterized reaction intermediate proposed to arise during the catalytic cycle of this class of enzymes. This work opens new perspectives for further deciphering the reaction mechanism of this nearly ubiquitous class of oxidoreductases.

Organizational Affiliation

Department of Chemical Sciences and Bernal Institute, University of Limerick, Ireland. Tewfik.soulimane@ul.ie.

Macromolecule Content

Total Structure Weight: 44.41 kDa
Atom Count: 3,485
Modeled Residue Count: 377
Deposited Residue Count: 386
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putaitve sulfite oxidase	A [auth AAA]	386	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: TTHA1325
UniProt
Find proteins for Q5SIP4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIP4 Go to UniProtKB: Q5SIP4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SIP4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MSS (Subject of Investigation/LOI) Query on MSS Download:Ideal Coordinates CCD File SDF format, chain B [auth AAA] MOL2 format, chain B [auth AAA] mmCIF format, chain B [auth AAA]	B [auth AAA]	(MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM C₁₀ H₁₂ Mo N₅ O₇ P S₂ BDXDYZBRBRKVRM-MRZGRPIRSA-L		Interactions Focus chain B [auth AAA] Interactions & Density Focus chain B [auth AAA]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth AAA] SDF format, chain H [auth AAA] SDF format, chain G [auth AAA] SDF format, chain F [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain F [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain F [auth AAA]	F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Interactions & Density Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth AAA] SDF format, chain E [auth AAA] SDF format, chain D [auth AAA] SDF format, chain C [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA], D [auth AAA], E [auth AAA], J [auth AAA]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain J [auth AAA] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain J [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.191 (Depositor), 0.196 (DCC)
R-Value Work: 0.166 (Depositor), 0.177 (DCC)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.6	α = 90
b = 130.6	β = 90
c = 114.59	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-08-05

Deposition Author(s):

Djeghader, A.

Soulimane, T.

Revision History (Full details and data files)

Version 1.0: 2020-08-05
Type: Initial release
Version 1.1: 2020-08-12
Changes: Database references
Version 1.2: 2020-09-02
Changes: Database references
Version 1.3: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description