4Q31

The crystal structure of cystathione gamma lyase (CalE6) from Micromonospora echinospora


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.099 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural dynamics of a methionine gamma-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate.

Cao, H.Tan, K.Wang, F.Bigelow, L.Yennamalli, R.M.Jedrzejczak, R.Babnigg, G.Bingman, C.A.Joachimiak, A.Kharel, M.K.Singh, S.Thorson, J.S.Phillips, G.N.

(2016) Struct Dyn 3: 034702-034702

  • DOI: 10.1063/1.4948539

  • PubMed Abstract: 
  • CalE6 from Micromonospora echinospora is a (pyridoxal 5' phosphate) PLP-dependent methionine γ-lyase involved in the biosynthesis of calicheamicins. We report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand ...

    CalE6 from Micromonospora echinospora is a (pyridoxal 5' phosphate) PLP-dependent methionine γ-lyase involved in the biosynthesis of calicheamicins. We report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand-induced rotation of Tyr100, which stacks with PLP, resembling the corresponding tyrosine rotation of true catalytic intermediates of CalE6 homologs. Elastic network modeling and crystallographic ensemble refinement reveal mobility of the N-terminal loop, which involves both tetrameric assembly and PLP binding. Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis and holoenzyme maturation.


    Organizational Affiliation

    Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cystathione gamma lyase CalE6
A, B, C, D, E, F, G, H
384Micromonospora echinosporaMutation(s): 1 
Gene Names: calE6
Find proteins for Q8KNG3 (Micromonospora echinospora)
Go to UniProtKB:  Q8KNG3
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, C, F, G, H
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
LLP
Query on LLP
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.099 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.152 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 146.855α = 90.00
b = 146.981β = 90.00
c = 349.905γ = 90.00
Software Package:
Software NamePurpose
SHELXDphasing
HKL-3000data scaling
ARPmodel building
MLPHAREphasing
DMmodel building
PHENIXrefinement
HKL-3000phasing
WARPmodel building
HKL-3000data reduction
SBC-Collectdata collection
DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2017-03-08
    Type: Database references