1KZH

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.243
R-Value Work: 0.203

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(02)00760-8
Primary Citation of 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.

Organizational Affiliation

Institute of Molecular Biosciences and Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand. s.morre@massey.ac.nz

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P70826
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A]	C [auth A] D [auth A] E [auth A] F [auth B] G [auth B] 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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.243
R-Value Work: 0.203
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2002-05-15

Deposition Author(s):

Revision History (Full details and data files)

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