3OPY

Crystal structure of Pichia pastoris phosphofructokinase in the T-state


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 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

    Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany. strater@bbz.uni-leipzig.de



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
6-phosphofructo-1-kinase alpha-subunitA, C, E, G989Komagataella pastoris DSMZ 70382Mutation(s): 0 
EC: 2.7.1.11
UniProt
Find proteins for Q8NJU8 (Komagataella pastoris)
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Go to UniProtKB:  Q8NJU8
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
6-phosphofructo-1-kinase beta-subunitB, D, F, H941Komagataella pastoris DSMZ 70382Mutation(s): 0 
EC: 2.7.1.11
UniProt
Find proteins for Q8TGA0 (Komagataella pastoris)
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Go to UniProtKB:  Q8TGA0
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
6-phosphofructo-1-kinase gamma-subunitI, J, K, L351Komagataella pastoris DSMZ 70382Mutation(s): 0 
EC: 2.7.1.11
UniProt
Find proteins for A7MAS3 (Komagataella pastoris)
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Go to UniProtKB:  A7MAS3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
KB [auth H], MA [auth D], YA [auth F], Z [auth B]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B] , AB [auth F] , AC [auth L] , BA [auth B] , BB [auth F] , BC [auth L] , CA [auth C] , CB [auth G] , 
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
 Ligand Interaction
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 = 161.658α = 90
b = 188.303β = 92.85
c = 231.56γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
BUSTERrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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