1TV2

Crystal structure of the hydroxylamine MtmB complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Reactivity and chemical synthesis of L-pyrrolysine- the 22(nd) genetically encoded amino acid

Hao, B.Zhao, G.Kang, P.T.Soares, J.A.Ferguson, T.K.Gallucci, J.Krzycki, J.A.Chan, M.K.

(2004) Chem Biol 11: 1317-1324

  • DOI: 10.1016/j.chembiol.2004.07.011
  • Primary Citation of Related Structures:  
    1TV2, 1TV4, 1TV3

  • PubMed Abstract: 
  • L-pyrrolysine, the 22(nd) genetically encoded amino acid, was previously deduced to be (4R, 5R)-4-substituted-pyrroline-5-carboxylate attached to the epsilon-nitrogen of lysine based on the crystal structure of the M. barkeri monomethylamine methyltransferase (MtmB) ...

    L-pyrrolysine, the 22(nd) genetically encoded amino acid, was previously deduced to be (4R, 5R)-4-substituted-pyrroline-5-carboxylate attached to the epsilon-nitrogen of lysine based on the crystal structure of the M. barkeri monomethylamine methyltransferase (MtmB). To confirm L-pyrrolysine's identity, structures of MtmB have been determined following treatment with hydroxylamine, N-methylhydroxylamine, or dithionite. Analysis of these structures has provided additional support for the presence of the pyrroline ring and, together with previous mass spectroscopy data, has led us to assign the C(4)-substituent to a methyl group. Based on this assignment, synthetic L-pyrrolysine was prepared by chemical methods. Detailed study of this chemically synthesized L-pyrrolysine has allowed us to characterize its physical properties, to study its chemical stability, and to elucidate the role of its C(4) substituent. Future applications of this synthetic L-pyrrolysine include its in vivo incorporation into recombinant proteins.


    Organizational Affiliation

    Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Monomethylamine methyltransferase mtmB1 A458Methanosarcina barkeriMutation(s): 0 
Gene Names: mtmB1mtmB
EC: 2.1.1 (PDB Primary Data), 2.1.1.248 (UniProt)
Find proteins for O30642 (Methanosarcina barkeri)
Explore O30642 
Go to UniProtKB:  O30642
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BG5
Query on BG5

Download Ideal Coordinates CCD File 
A
5-HYDROXYAMINO-3-METHYL-PYRROLIDINE-2-CARBOXYLIC ACID
C6 H12 N2 O3
PEFGUPQPFCDBPY-UOWFLXDJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.17α = 90
b = 158.17β = 90
c = 136.21γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-19
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model