Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Hetero 12-mer - A4B4C4 Pseudo Symmetry: Dihedral - D2  (3D View)
Pseudo Stoichiometry: Hetero 12-mer - A8B4 

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

Macromolecule Content

• Total Structure Weight: 1,022.79 kDa 
• Atom Count: 65,025 
• Modelled Residue Count: 8,572 
• Deposited Residue Count: 9,124 
• Unique protein chains: 3

 3OPY

Crystal structure of Pichia pastoris phosphofructokinase in the T-state

• PDB DOI:  https://doi.org/10.2210/pdb3OPY/pdb

• Classification: TRANSFERASE
• Organism(s): Komagataella pastoris DSMZ 70382
• Mutation(s): No 


• Deposited: 2010-09-02 Released: 2010-10-06 
• Deposition Author(s): Strater, N., Marek, S., Kuettner, E.B., Kloos, M., Keim, A., Bruser, A., Kirchberger, J., Schoneberg, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.232 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Molecular architecture and structural basis of allosteric regulation of eukaryotic phosphofructokinases.

Strater, N., Marek, S., Kuettner, E.B., Kloos, M., Keim, A., Bruser, A., Kirchberger, J., Schoneberg, T.

(2011) FASEB J 25: 89-98

• PubMed: 20833871 
• DOI: https://doi.org/10.1096/fj.10-163865
• Primary Citation of Related Structures:  
  3OPY


• PubMed Abstract: 
  

Eukaryotic ATP-dependent 6-phosphofructokinases (Pfks) differ from their bacterial counterparts in a much more complex structural organization and allosteric regulation. Pichia pastoris Pfk (PpPfk) is, with ∼ 1 MDa, the most complex and probably largest eukaryotic Pfk. We have determined the crystal structure of full-length PpPfk to 3.05 Å resolution in the T state. PpPfk forms a (αβγ)(4) dodecamer of D(2) symmetry with dimensions of 161 × 157 × 233 Å mainly via interactions of the α chains. The N-terminal domains of the α and β chains have folds that are distantly related to glyoxalase I, but the active sites are no longer functional. Interestingly, these domains located at the 2 distal ends of this protein along the long 2-fold axis form a (αβ)(2) dimer as does the core Pfk domains; however, the domains are swapped across the tetramerization interface. In PpPfk, the unique γ subunit participates in oligomerization of the αβ chains. This modulator protein was acquired from an ancient S-adenosylmethionine-dependent methyltransferase. The identification of novel ATP binding sites, which do not correspond to the bacterial catalytic or effector binding sites, point to marked structural and functional differences between bacterial and eukaryotic Pfks.

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Organizational Affiliation: 

Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphofructo-1-kinase alpha-subunit	A, C, E, G	989	Komagataella pastoris DSMZ 70382	Mutation(s): 0  EC: 2.7.1.11
UniProt
Find proteins for Q8NJU8 (Komagataella pastoris) Explore Q8NJU8  Go to UniProtKB:  Q8NJU8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphofructo-1-kinase beta-subunit	B, D, F, H	941	Komagataella pastoris DSMZ 70382	Mutation(s): 0  EC: 2.7.1.11
UniProt
Find proteins for Q8TGA0 (Komagataella pastoris) Explore Q8TGA0  Go to UniProtKB:  Q8TGA0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphofructo-1-kinase gamma-subunit	I, J, K, L	351	Komagataella pastoris DSMZ 70382	Mutation(s): 0  EC: 2.7.1.11
UniProt
Find proteins for A7MAS3 (Komagataella pastoris) Explore A7MAS3  Go to UniProtKB:  A7MAS3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	KB [auth H], MA [auth D], YA [auth F], Z [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SO4	AA [auth B], AB [auth F], AC [auth L], BA [auth B], BB [auth F], BC [auth L], CA [auth C], CB [auth G], CC [auth L], DA [auth C], DB [auth G], EA [auth C], EB [auth G], FA [auth C], FB [auth G], GA [auth C], GB [auth G], HA [auth C], HB [auth G], IA [auth C], IB [auth G], JA [auth C], JB [auth G], KA [auth C], LA [auth C], LB [auth H], M [auth A], MB [auth H], N [auth A], NA [auth D], NB [auth H], O [auth A], OA [auth D], OB [auth H], P [auth A], PA [auth D], PB [auth I], Q [auth A], QA [auth E], QB [auth I], R [auth A], RA [auth E], RB [auth I], S [auth A], SA [auth E], SB [auth I], T [auth A], TA [auth E], TB [auth I], U [auth A], UA [auth E], UB [auth J], V [auth A], VA [auth E], VB [auth J], W [auth A], WA [auth E], WB [auth J], X [auth A], XA [auth E], XB [auth K], Y [auth A], YB [auth K], ZA [auth F], ZB [auth K]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.232 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.658	α = 90
b = 188.303	β = 92.85
c = 231.56	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
BUSTER	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-06 
Deposition Author(s): Strater, N., Marek, S., Kuettner, E.B., Kloos, M., Keim, A., Bruser, A., Kirchberger, J., Schoneberg, T.

Revision History  

• Version 1.0: 2010-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance