6KJI

Crystal structure of PsoF with SAH

PDB DOI: https://doi.org/10.2210/pdb6KJI/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aspergillus fumigatus Af293
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-07-22 Released: 2019-09-18
Deposition Author(s): Hara, K., Hashimoto, H., Matsushita, T., Tsunematsu, Y., Watanabe, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.214
R-Value Work: 0.172
R-Value Observed: 0.174

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Ligand Structure Quality Assessment

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

Literature

Functional and Structural Analyses oftrans C-Methyltransferase in Fungal Polyketide Biosynthesis.

Kishimoto, S., Tsunematsu, Y., Matsushita, T., Hara, K., Hashimoto, H., Tang, Y., Watanabe, K.

(2019) Biochemistry 58: 3933-3937

PubMed: 31486637 Search on PubMed
DOI: https://doi.org/10.1021/acs.biochem.9b00702
Primary Citation of Related Structures:
6KJG, 6KJI

PubMed Abstract:
Biosynthesis of certain fungal polyketide-peptide synthetases involves C -methyltransferase activity that adds one or more S -adenosyl-l-methionine-derived methyl groups to the carbon framework. The previously reported PsoF-MT, the stand-alone C -methyltransferase (MT) from the pseurotin biosynthetic pathway that exists as a domain within a trifunctional didomain enzyme PsoF, was characterized crystallographically and kinetically using mutants with substrate analogs to understand how a trans -acting C -MT works and compare it to known polyketide synthase-associated C -MTs. This study identified key active-site residues involved in catalysis and substrate recognition, which led us to propose the mechanism of C -methylation and substrate specificity determinants in PsoF-MT.

Organizational Affiliation

Department of Pharmaceutical Sciences , University of Shizuoka , Shizuoka 422-8526 , Japan.

Macromolecule Content

Total Structure Weight: 126.93 kDa
Atom Count: 8,996
Modelled Residue Count: 1,049
Deposited Residue Count: 1,134
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual-functional monooxygenase/methyltransferase psoF	A, B, C	378	Aspergillus fumigatus Af293	Mutation(s): 0 Gene Names: psoF, AFUA_8G00440 EC: 1 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt
Find proteins for Q4WAZ0 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)) Explore Q4WAZ0 Go to UniProtKB: Q4WAZ0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4WAZ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C]	D [auth A], G [auth B], J [auth C]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain J [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C]	E [auth A] F [auth A] H [auth B] I [auth B] K [auth C] E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.214
R-Value Work: 0.172
R-Value Observed: 0.174
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.873	α = 90
b = 44.036	β = 93.24
c = 143.124	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-09-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-09-18
Type: Initial release
Version 1.1: 2019-10-02
Changes: Data collection, Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description