Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 94.24 kDa 
• Atom Count: 6725 
• Modelled Residue Count: 786 
• Deposited Residue Count: 826 
• Unique protein chains: 1

3GFX

Klebsiella pneumoniae BlrP1 pH 4.5 calcium/cy-diGMP complex

• PDB DOI: 10.2210/pdb3GFX/pdb

• Classification: HYDROLASE, SIGNALING PROTEIN
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-27 Released: 2009-06-23 
• Deposition Author(s): Barends, T., Hartmann, E., Griese, J., Beitlich, T., Kirienko, N., Ryjenkov, D., Reinstein, J., Shoeman, R., Gomelsky, M., Schlichting, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.277 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Literature

Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase.

Barends, T.R., Hartmann, E., Griese, J.J., Beitlich, T., Kirienko, N.V., Ryjenkov, D.A., Reinstein, J., Shoeman, R.L., Gomelsky, M., Schlichting, I.

(2009) Nature 459: 1015-1018

• PubMed: 19536266 
• DOI: 10.1038/nature07966
• Primary Citation of Related Structures:  
  3GFX, 3GFY, 3GFZ, 3GG0, 3GG1


• PubMed Abstract: 
  

The ability to respond to light is crucial for most organisms. BLUF is a recently identified photoreceptor protein domain that senses blue light using a FAD chromophore. BLUF domains are present in various proteins from the Bacteria, Euglenozoa and Fungi. Although structures of single-domain BLUF proteins have been determined, none are available for a BLUF protein containing a functional output domain; the mechanism of light activation in this new class of photoreceptors has thus remained poorly understood. Here we report the biochemical, structural and mechanistic characterization of a full-length, active photoreceptor, BlrP1 (also known as KPN_01598), from Klebsiella pneumoniae. BlrP1 consists of a BLUF sensor domain and a phosphodiesterase EAL output domain which hydrolyses cyclic dimeric GMP (c-di-GMP). This ubiquitous second messenger controls motility, biofilm formation, virulence and antibiotic resistance in the Bacteria. Crystal structures of BlrP1 complexed with its substrate and metal ions involved in catalysis or in enzyme inhibition provide a detailed understanding of the mechanism of the EAL-domain c-di-GMP phosphodiesterases. These structures also sketch out a path of light activation of the phosphodiesterase output activity. Photon absorption by the BLUF domain of one subunit of the antiparallel BlrP1 homodimer activates the EAL domain of the second subunit through allosteric communication transmitted through conserved domain-domain interfaces.

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Organizational Affiliation: 

Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Jahnstrasse 29, 69120 Heidelberg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Klebsiella pneumoniae BlrP1	A, B	413	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0  Gene Names: blrp1, KPN78578_15680, KPN_01598
UniProt
Find proteins for A6T8V8 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6T8V8  Go to UniProtKB:  A6T8V8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2E	D [auth A], G [auth B]	9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) C20 H24 N10 O14 P2 PKFDLKSEZWEFGL-MHARETSRSA-N
FMN	C [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
CA	E [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.277 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69	α = 90
b = 96.9	β = 90
c = 128.5	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
autoSHARP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-02-27 
• Released Date: 2009-06-23 
Deposition Author(s): Barends, T., Hartmann, E., Griese, J., Beitlich, T., Kirienko, N., Ryjenkov, D., Reinstein, J., Shoeman, R., Gomelsky, M., Schlichting, I.

Revision History  

• Version 1.0: 2009-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-06-19
  Changes: Database references
• Version 1.3: 2017-11-01
  Changes: Refinement description