5WMM

Crystal structure of an adenylation domain interrupted by a methylation domain (AMA4) from nonribosomal peptide synthetase TioS

PDB DOI: https://doi.org/10.2210/pdb5WMM/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Micromonospora sp. ML1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-07-30 Released: 2018-03-14
Deposition Author(s): Pang, A.H., Mori, S., Garneau-Tsodikova, S., Tsodikov, O.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.253
R-Value Work: 0.236
R-Value Observed: 0.237

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural basis for backbone N-methylation by an interrupted adenylation domain.

Mori, S., Pang, A.H., Lundy, T.A., Garzan, A., Tsodikov, O.V., Garneau-Tsodikova, S.

(2018) Nat Chem Biol 14: 428-430

PubMed: 29556104 Search on PubMed
DOI: https://doi.org/10.1038/s41589-018-0014-7
Primary Citation of Related Structures:
5WMM

PubMed Abstract:
Interrupted adenylation domains are enigmatic fusions, in which one enzyme is inserted into another to form a highly unusual bifunctional enzyme. We present the first crystal structure of an interrupted adenylation domain that reveals a unique embedded methyltransferase. The structure and functional data provide insight into how these enzymes N-methylate amino acid precursors en route to nonribosomal peptides.

Organizational Affiliation

Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.

Macromolecule Content

Total Structure Weight: 112.95 kDa
Atom Count: 7,342
Modelled Residue Count: 934
Deposited Residue Count: 1,013
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NRPS	A	926	Micromonospora sp. ML1	Mutation(s): 0 Gene Names: tioS
UniProt
Find proteins for Q333U7 (Micromonospora sp. ML1) Explore Q333U7 Go to UniProtKB: Q333U7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q333U7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MbtH homologue	B	87	Micromonospora sp. ML1	Mutation(s): 0 Gene Names: tioT
UniProt
Find proteins for Q333U6 (Micromonospora sp. ML1) Explore Q333U6 Go to UniProtKB: Q333U6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q333U6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B6G Query on B6G Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	(2S)-2-amino-3-methylbutanoyl (2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl hydrogen (S)-phosphate C₁₄ H₂₁ N₆ O₈ P PJUFCHCQTYUTMG-JDUCOKCXSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	H [auth A], I [auth A], J [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.253
R-Value Work: 0.236
R-Value Observed: 0.237
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.712	α = 90
b = 136.712	β = 90
c = 228.234	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-03-14

Deposition Author(s):

Pang, A.H.

Mori, S.

Garneau-Tsodikova, S.

Tsodikov, O.V.

Revision History (Full details and data files)

Version 1.0: 2018-03-14
Type: Initial release
Version 1.1: 2018-04-04
Changes: Data collection, Database references
Version 1.2: 2018-04-25
Changes: Data collection, Database references
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description