1KZH | pdb_00001kzh

Structure of a pyrophosphate-dependent phosphofructokinase from the Lyme disease spirochete Borrelia burgdorferi

• PDB DOI: https://doi.org/10.2210/pdb1KZH/pdb

• Classification: TRANSFERASE
• Organism(s): Borreliella burgdorferi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-02-06 Released: 2002-05-15 
• Deposition Author(s): Moore, S.A., Ronimus, R.S., Roberson, R.S., Morgan, H.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.202 (DCC) 

Literature

The structure of a pyrophosphate-dependent phosphofructokinase from the Lyme disease spirochete Borrelia burgdorferi.

Moore, S.A., Ronimus, R.S., Roberson, R.S., Morgan, H.W.

(2002) Structure 10: 659-671

• PubMed: 12015149 
• DOI: https://doi.org/10.1016/s0969-2126(02)00760-8
• Primary Citation Related Structures: 
  1KZH


• PubMed Abstract: 
  

  The structure of the 60 kDa pyrophosphate (PP(i))-dependent phosphofructokinase (PFK) from Borrelia burgdorferi has been solved and refined (R(free) = 0.243) at 2.55 A resolution. The domain structure of eubacterial ATP-dependent PFKs is conserved in B. burgdorferi PFK, and there are three large insertions relative to E. coli PFK, including a helical domain containing a hairpin structure that interacts with the active site. Asp177, conserved in all PP(i) PFKs, negates the binding of the alpha-phosphate group of ATP and likely contacts the essential Mg(2+) cation via a water molecule. Asn181 blocks the binding of the adenine moiety of ATP. Lys203 hydrogen bonds to a sulfate anion that likely mimics PP(i) substrate binding.

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Organizational Affiliation: 
• Institute of Molecular Biosciences and Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 125.87 kDa 
• Atom Count: 8,512 
• Modeled Residue Count: 1,080 
• Deposited Residue Count: 1,110 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phosphofructokinase	A, B	555	Borreliella burgdorferi	Mutation(s): 0  Gene Names: BB0020 EC: 2.7.1.90
UniProt
Find proteins for P70826 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31)) Explore P70826  Go to UniProtKB:  P70826

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.202 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.098	α = 90
b = 97.926	β = 90
c = 148.173	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	data scaling
SIGMAA	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-15 
Deposition Author(s): Moore, S.A., Ronimus, R.S., Roberson, R.S., Morgan, H.W.

Revision History  

• Version 1.0: 2002-05-15
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2019-02-06
  Changes: Data collection, Database references, Source and taxonomy, Structure summary
• Version 1.5: 2024-03-13
  Changes: Data collection, Database references, Derived calculations