4G37

Structure of cross-linked firefly luciferase in second catalytic conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.396 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of firefly luciferase in a second catalytic conformation supports a domain alternation mechanism.

Sundlov, J.A.Fontaine, D.M.Southworth, T.L.Branchini, B.R.Gulick, A.M.

(2012) Biochemistry 51: 6493-6495

  • DOI: 10.1021/bi300934s
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Beetle luciferases catalyze a two-step reaction that includes the initial adenylation of the luciferin substrate, followed by an oxidative decarboxylation that ultimately produces light. Evidence for homologous acyl-CoA synthetases supports a domain ...

    Beetle luciferases catalyze a two-step reaction that includes the initial adenylation of the luciferin substrate, followed by an oxidative decarboxylation that ultimately produces light. Evidence for homologous acyl-CoA synthetases supports a domain alternation catalytic mechanism in which these enzymes' C-terminal domain rotates by ~140° to adopt two conformations that are used to catalyze the two partial reactions. While many structures exist of acyl-CoA synthetases in both conformations, to date only biochemical evidence supports domain alternation with luciferase. We have determined the structure of a cross-linked luciferase enzyme that is trapped in the second conformation. This new structure supports the role of the second catalytic conformation and provides insights into the biochemical mechanism of the luciferase oxidative step.


    Organizational Affiliation

    Hauptman-Woodward Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Luciferin 4-monooxygenase
A, B
555Photinus pyralisMutation(s): 11 
EC: 1.13.12.7
Find proteins for P08659 (Photinus pyralis)
Go to UniProtKB:  P08659
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XLX
Query on XLX

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A, B
4,4'-(ethylenediimino)bis[4-oxobutyrate]
1,2-bis(maleimido)ethane, hydrolyzed open form
C11 H18 N2 O6
JUHMDCQKNGDTCV-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
SLU
Query on SLU

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Download CCD File 
A, B
5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE
C21 H18 N8 O8 S3
LJLYTUYNVSHXQB-SOONXTGKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.396 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 75.638α = 90.00
b = 184.091β = 90.00
c = 170.530γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2012-10-31
    Type: Database references