4Q3E

PylD cocrystallized with L-Ornithine-Nd-D-lysine and NAD+

PDB DOI: https://doi.org/10.2210/pdb4Q3E/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: 2.20 Å
R-Value Free: 0.215
R-Value Work: 0.178
R-Value Observed: 0.180

Starting Model: experimental
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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: 58.24 kDa
Atom Count: 4,187
Modelled Residue Count: 508
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PYLD, pyrrolysine synthase	A, B	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 C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
2YJ Query on 2YJ Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	F [auth A], M [auth B]	N~5~-D-lysyl-L-ornithine C₁₁ H₂₄ N₄ O₃ IIZZYHGWMHUAMZ-BDAKNGLRSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B]	G [auth A], H [auth A], O [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	E [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	D [auth A], K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.215
R-Value Work: 0.178
R-Value Observed: 0.180
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.08	α = 90
b = 210.46	β = 90
c = 77.64	γ = 90

Software Package:

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

Structure Validation

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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: 2014-07-02
Changes: Database references
Version 1.2: 2014-08-20
Changes: Database references
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-06
Changes: Structure summary

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Help and Resources

4Q3E

PylD cocrystallized with L-Ornithine-Nd-D-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

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)