4Q3A | pdb_00004q3a

PylD cocrystallized with L-Lysine-Ne-3S-methyl-L-ornithine and NAD+

PDB DOI: https://doi.org/10.2210/pdb4Q3A/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:
0.204 (Depositor), 0.210 (DCC)
R-Value Work:
0.169 (Depositor), 0.178 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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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 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: 118.33 kDa
Atom Count: 8,575
Modeled Residue Count: 1,037
Deposited Residue Count: 1,040
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q46E80
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain WA [auth D] SDF format, chain T [auth B] SDF format, chain OA [auth C] SDF format, chain E [auth A] MOL2 format, chain WA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain OA [auth C] MOL2 format, chain E [auth A] mmCIF format, chain WA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain OA [auth C] mmCIF format, chain E [auth A]	E [auth A], OA [auth C], T [auth B], WA [auth D]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain OA [auth C] Focus chain T [auth B] Focus chain WA [auth D] Interactions & Density Focus chain E [auth A] Focus chain OA [auth C] Focus chain T [auth B] Focus chain WA [auth D]
2YC Query on 2YC Download:Ideal Coordinates CCD File SDF format, chain ZA [auth D] SDF format, chain W [auth B] SDF format, chain RA [auth C] SDF format, chain H [auth A] MOL2 format, chain ZA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain H [auth A] mmCIF format, chain ZA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain RA [auth C] mmCIF format, chain H [auth A]	H [auth A], RA [auth C], W [auth B], ZA [auth D]	N~6~-{[(2S,3S)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine C₁₂ H₂₁ N₃ O₃ ZFOMKMMPBOQKMC-GUBZILKMSA-N		Interactions Focus chain H [auth A] Focus chain RA [auth C] Focus chain W [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain H [auth A] Focus chain RA [auth C] Focus chain W [auth B] Focus chain ZA [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain GA [auth B] SDF format, chain FA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B]	FA [auth B], GA [auth B], P [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain GA [auth B] Focus chain P [auth A] Interactions & Density Focus chain FA [auth B] Focus chain GA [auth B] Focus chain P [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B]	DA [auth B], EA [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain SA [auth C] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] I [auth A] J [auth A] AA [auth B], BA [auth B], CA [auth B], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], SA [auth C], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain SA [auth C] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain SA [auth C] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain VA [auth C] SDF format, chain UA [auth C] SDF format, chain TA [auth C] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain NA [auth B] SDF format, chain MA [auth B] SDF format, chain LA [auth B] SDF format, chain KA [auth B] SDF format, chain JA [auth B] SDF format, chain IA [auth B] SDF format, chain HA [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] mmCIF format, chain VA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B]	HA [auth B] IA [auth B] JA [auth B] KA [auth B] LA [auth B] HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth B], Q [auth A], R [auth A], S [auth A], TA [auth C], UA [auth C], VA [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Interactions & Density Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain YA [auth D] SDF format, chain V [auth B] SDF format, chain QA [auth C] SDF format, chain G [auth A] MOL2 format, chain YA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain G [auth A] mmCIF format, chain YA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain QA [auth C] mmCIF format, chain G [auth A]	G [auth A], QA [auth C], V [auth B], YA [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain QA [auth C] Focus chain V [auth B] Focus chain YA [auth D] Interactions & Density Focus chain G [auth A] Focus chain QA [auth C] Focus chain V [auth B] Focus chain YA [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain XA [auth D] SDF format, chain U [auth B] SDF format, chain PA [auth C] SDF format, chain F [auth A] MOL2 format, chain XA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain F [auth A] mmCIF format, chain XA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain PA [auth C] mmCIF format, chain F [auth A]	F [auth A], PA [auth C], U [auth B], XA [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain PA [auth C] Focus chain U [auth B] Focus chain XA [auth D] Interactions & Density Focus chain F [auth A] Focus chain PA [auth C] Focus chain U [auth B] Focus chain XA [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.204 (Depositor), 0.210 (DCC)
R-Value Work: 0.169 (Depositor), 0.178 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.49	α = 90
b = 259.85	β = 90
c = 48.66	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

View more in-depth experimental data

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: 2024-10-16
Changes: Structure summary