4Q3C

PylD cocrystallized with L-Lysine-Ne-L-lysine and NAD+

PDB DOI: https://doi.org/10.2210/pdb4Q3C/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methanosarcina barkeri str. Fusaro
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-04-11 Released: 2014-04-23
Deposition Author(s): Quitterer, F., Beck, P., Bacher, A., Groll, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.198
R-Value Work: 0.169
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed by Pyrrolysine Synthase (PylD).

Quitterer, F., Beck, P., Bacher, A., Groll, M.

(2014) Angew Chem Int Ed Engl 53: 8150-8153

PubMed: 24916332 Search on PubMed
DOI: https://doi.org/10.1002/anie.201402595
Primary Citation of Related Structures:
4Q39, 4Q3A, 4Q3B, 4Q3C, 4Q3D, 4Q3E

PubMed Abstract:
The dehydrogenase PylD catalyzes the ultimate step of the pyrrolysine pathway by converting the isopeptide L-lysine-Nε-3R-methyl-D-ornithine to the 22nd proteinogenic amino acid. In this study, we demonstrate how PylD can be harnessed to oxidize various isopeptides to novel amino acids by combining chemical synthesis with enzyme kinetics and X-ray crystallography. The data enable a detailed description of the PylD reaction trajectory for the biosynthesis of pyrroline and tetrahydropyridine rings as constituents of pyrrolysine analogues.

Organizational Affiliation

Center for Integrated Protein Science Munich (CIPSM), Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching (Germany).

Macromolecule Content

Total Structure Weight: 116.46 kDa
Atom Count: 8,384
Modelled Residue Count: 1,035
Deposited Residue Count: 1,040
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PylD, pyrrolysine synthase	A, B, C, D	260	Methanosarcina barkeri str. Fusaro	Mutation(s): 0 Gene Names: Mbar_A0835 EC: 1.4.1
UniProt
Find proteins for Q46E80 (Methanosarcina barkeri (strain Fusaro / DSM 804)) Explore Q46E80 Go to UniProtKB: Q46E80
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q46E80
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D]	E [auth A], O [auth B], U [auth C], Y [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain Y [auth D]
2YG Query on 2YG Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain H [auth A] SDF format, chain R [auth B] SDF format, chain X [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain R [auth B] MOL2 format, chain X [auth C]	BA [auth D], H [auth A], R [auth B], X [auth C]	N~6~-L-lysyl-L-lysine C₁₂ H₂₆ N₄ O₃ ISWYJQKGNGBKJG-UWVGGRQHSA-N		Interactions Focus chain BA [auth D] Focus chain H [auth A] Focus chain R [auth B] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain H [auth A] Focus chain R [auth B] Focus chain X [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B]	T [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain S [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B]	I [auth A], J [auth A], K [auth A], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A]	L [auth A], M [auth A], N [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain G [auth A] SDF format, chain Q [auth B] SDF format, chain W [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C]	AA [auth D], G [auth A], Q [auth B], W [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain G [auth A] Focus chain Q [auth B] Focus chain W [auth C] Interactions & Density Focus chain AA [auth D] Focus chain G [auth A] Focus chain Q [auth B] Focus chain W [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain P [auth B] SDF format, chain V [auth C] SDF format, chain Z [auth D] MOL2 format, chain F [auth A] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D]	F [auth A], P [auth B], V [auth C], Z [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain P [auth B] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain P [auth B] Focus chain V [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.198
R-Value Work: 0.169
R-Value Observed: 0.170
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.25	α = 90
b = 259.77	β = 90
c = 48.93	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-04-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-23
Type: Initial release
Version 1.1: 2014-04-30
Changes: Structure summary
Version 1.2: 2014-07-02
Changes: Database references
Version 1.3: 2014-08-20
Changes: Database references
Version 1.4: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

4Q3C

PylD cocrystallized with L-Lysine-Ne-L-lysine and NAD+

The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed by Pyrrolysine Synthase (PylD).

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)