4G37 | pdb_00004g37

Structure of cross-linked firefly luciferase in second catalytic conformation

PDB DOI: https://doi.org/10.2210/pdb4G37/pdb

Classification: LIGASE
Organism(s): Photinus pyralis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-07-13 Released: 2012-08-15
Deposition Author(s): Sundlov, J.A., Branchini, B.R., Gulick, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.259 (Depositor), 0.249 (DCC)
R-Value Work:
0.199 (Depositor), 0.191 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 22852753 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/bi300934s
Primary Citation Related Structures:
4G36, 4G37

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 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.

Macromolecule Content

Total Structure Weight: 124.21 kDa
Atom Count: 8,395
Modeled Residue Count: 1,072
Deposited Residue Count: 1,110
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Luciferin 4-monooxygenase	A, B	555	Photinus pyralis	Mutation(s): 11 EC: 1.13.12.7
UniProt
Find proteins for P08659 (Photinus pyralis) Explore P08659 Go to UniProtKB: P08659
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08659
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SLU Query on SLU Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE C₂₁ H₁₈ N₈ O₈ S₃ LJLYTUYNVSHXQB-SOONXTGKSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
XLX Query on XLX Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	4,4'-(ethylenediimino)bis[4-oxobutyrate] C₁₁ H₁₈ N₂ O₆ JUHMDCQKNGDTCV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth A], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.259 (Depositor), 0.249 (DCC)
R-Value Work: 0.199 (Depositor), 0.191 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.638	α = 90
b = 184.091	β = 90
c = 170.53	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-08-15

Deposition Author(s):

Sundlov, J.A.

Branchini, B.R.

Gulick, A.M.

Revision History (Full details and data files)

Version 1.0: 2012-08-15
Type: Initial release
Version 1.1: 2012-10-31
Changes: Database references
Version 1.2: 2023-09-13
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary