8C49

Crystal structure of pyrrolysyl-tRNA synthetase from Methanomethylophilus alvus engineered for 3-Methyl-L-histidine, bound to AMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Engineering mutually orthogonal PylRS/tRNA pairs for dual encoding of functional histidine analogues.

Taylor, C.J.Hardy, F.J.Burke, A.J.Bednar, R.M.Mehl, R.A.Green, A.P.Lovelock, S.L.

(2023) Protein Sci 32: e4640-e4640

  • DOI: https://doi.org/10.1002/pro.4640
  • Primary Citation of Related Structures:  
    8C49

  • PubMed Abstract: 

    The availability of an expanded genetic code opens exciting new opportunities in enzyme design and engineering. In this regard histidine analogues have proven particularly versatile, serving as ligands to augment metalloenzyme function and as catalytic nucleophiles in designed enzymes. The ability to genetically encode multiple functional residues could greatly expand the range of chemistry accessible within enzyme active sites. Here, we develop mutually orthogonal translation components to selectively encode two structurally similar histidine analogues. Transplanting known mutations from a promiscuous Methanosarcina mazei pyrrolysyl-tRNA synthetase (MmPylRS IFGFF ) into a single domain PylRS from Methanomethylophilus alvus (MaPylRS IFGFF ) provided a variant with improved efficiency and specificity for 3-methyl-L-histidine (MeHis) incorporation. The MaPylRS IFGFF clone was further characterized using in vitro biochemical assays and x-ray crystallography. We subsequently engineered the orthogonal MmPylRS for activity and selectivity for 3-(3-pyridyl)-L-alanine (3-Pyr), which was used in combination with MaPylRS IFGFF to produce proteins containing both 3-Pyr and MeHis. Given the versatile roles played by histidine in enzyme mechanisms, we anticipate that the tools developed within this study will underpin the development of enzymes with new and enhanced functions.


  • Organizational Affiliation

    Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrrolysyl-tRNA synthetase
A, B
283Methanomethylophilus alviMutation(s): 5 
Gene Names: MMALV_11280
EC: 6.1.1.26
UniProt
Find proteins for M9SC49 (Methanomethylophilus alvi (strain Mx1201))
Explore M9SC49 
Go to UniProtKB:  M9SC49
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM9SC49
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
C [auth A],
Q [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A],
W [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A]
H [auth A]
I [auth A]
J [auth A]
P [auth B]
D [auth A],
H [auth A],
I [auth A],
J [auth A],
P [auth B],
S [auth B],
U [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
R [auth B],
T [auth B],
V [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
K [auth A]
L [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
X [auth B],
Y [auth B],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.932α = 90
b = 59.932β = 90
c = 263.231γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
UK Research and Innovation (UKRI)United KingdomMR/T041722/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description