6JLS | pdb_00006jls

Crystal Structure of FMN-dependent Cysteine Decarboxylases TvaF from Thioviridamide Biosynthesis

PDB DOI: https://doi.org/10.2210/pdb6JLS/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces olivoviridis
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2019-03-06 Released: 2019-06-26
Deposition Author(s): Li, J., Lu, J., Wang, H., Zhu, J.
Funding Organization(s): National Science Foundation (China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free:
0.232 (Depositor), 0.236 (DCC)
R-Value Work:
0.216 (Depositor), 0.218 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Characterization of the FMN-Dependent Cysteine Decarboxylase from Thioviridamide Biosynthesis.

Lu, J., Li, J., Wu, Y., Fang, X., Zhu, J., Wang, H.

(2019) Org Lett 21: 4676-4679

PubMed: 31184189 Search on PubMed
DOI: https://doi.org/10.1021/acs.orglett.9b01531
Primary Citation Related Structures:
6JLS

PubMed Abstract:
The biosynthesis of thioviridamide-like compounds has not been elucidated. Herein, we report that TvaF from the thioviridamide biosynthetic gene cluster is an FMN-dependent cysteine decarboxylase that transforms the C-terminal cysteine of precursor peptides into a thioenol motif and exhibits high substrate flexibility. We resolved the crystal structure of TvaF bound with FMN at 2.24 Å resolution. Key residues for FMN binding and catalytic activity of TvaF have been identified and evaluated by mutagenesis studies.

Organizational Affiliation

State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China.

Macromolecule Content

Total Structure Weight: 20.86 kDa
Atom Count: 1,252
Modeled Residue Count: 162
Deposited Residue Count: 200
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative flavoprotein decarboxylase	A	200	Streptomyces olivoviridis	Mutation(s): 0 Gene Names: tvaF
UniProt
Find proteins for T2HUM4 (Streptomyces olivoviridis) Explore T2HUM4 Go to UniProtKB: T2HUM4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	T2HUM4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN 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]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.232 (Depositor), 0.236 (DCC)
R-Value Work: 0.216 (Depositor), 0.218 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 216.915	α = 90
b = 216.915	β = 90
c = 216.915	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-06-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (China)	China	--

Revision History (Full details and data files)

Version 1.0: 2019-06-26
Type: Initial release
Version 1.1: 2019-07-10
Changes: Data collection, Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description