4Q3D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


This is version 1.2 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

  • DOI: 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 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).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PYLD, pyrrolysine synthaseA, B, C, D260Methanosarcina barkeri str. FusaroMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46E80
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A],
N [auth B],
S [auth C],
W [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
2YH
Query on 2YH

Download Ideal Coordinates CCD File 
H [auth A],
Q [auth B],
V [auth C],
Z [auth D]
N~5~-D-ornithyl-L-ornithine
C10 H22 N4 O3
MCMLHDBHZRLOED-SFYZADRCSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth A],
R [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
P [auth B],
U [auth C],
Y [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
O [auth B],
T [auth C],
X [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.93α = 90
b = 259.32β = 90
c = 48.82γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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