4IMA

The structure of C436M-hLPYK in complex with Citrate/Mn/ATP/Fru-1,6-BP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Energetic Coupling between an Oxidizable Cysteine and the Phosphorylatable N-Terminus of Human Liver Pyruvate Kinase.

Holyoak, T.Zhang, B.Deng, J.Tang, Q.Prasannan, C.B.Fenton, A.W.

(2013) Biochemistry 52: 466-476

  • DOI: 10.1021/bi301341r
  • Primary Citation of Related Structures:  
    4IMA, 4IP7

  • PubMed Abstract: 
  • During our efforts to characterize the regulatory properties of human liver pyruvate kinase (L-PYK), we have noted that the affinity of the protein for phosphoenolpyruvate (PEP) becomes reduced several days after cell lysis. A 1.8 Å crystallographic structure of L-PYK with the S12D mimic of phosphorylation indicates that Cys436 is oxidized, the first potential insight into explaining the effect of "aging" ...

    During our efforts to characterize the regulatory properties of human liver pyruvate kinase (L-PYK), we have noted that the affinity of the protein for phosphoenolpyruvate (PEP) becomes reduced several days after cell lysis. A 1.8 Å crystallographic structure of L-PYK with the S12D mimic of phosphorylation indicates that Cys436 is oxidized, the first potential insight into explaining the effect of "aging". Interestingly, the oxidation is only to sulfenic acid despite the crystal growth time period of 2 weeks. Mutagenesis confirms that the side chain of residue 436 is energetically coupled to PEP binding. Mass spectrometry confirms that the oxidation is present in solution and is not an artifact caused by X-ray exposure. Exposure of the L-PYK mutations to H₂O₂ also confirms that PEP affinity is sensitive to the nature of the side chain at position 436. A 1.95 Å structure of the C436M mutant of L-PYK, the only mutation at position 436 that has been shown to strengthen PEP affinity, revealed that the methionine substitution results in the ordering of several N-terminal residues that have not been ordered in previous structures. This result allowed speculation that oxidation of Cys436 and phosphorylation of the N-terminus at Ser12 may function through a similar mechanism, namely the interruption of an activating interaction between the nonphosphorylated N-terminus with the nonoxidized main body of the protein. Mutant cycles were used to provide evidence that mutations of Cys436 are energetically synergistic with N-terminal modifications, a result that is consistent with phosphorylation of the N-terminus and oxidation of Cys436 functioning through mechanisms with common features. Alanine-scanning mutagenesis was used to confirm that the newly ordered N-terminal residues were important to the regulation of enzyme function by the N-terminus of the enzyme (i.e., not an artifact caused by the introduced methionine substitution) and to further define which residues in the N-terminus are energetically coupled to PEP affinity. Collectively, these studies indicate energetic coupling (and potentially mechanistic similarities) between the oxidation of Cys436 and phosphorylation of Ser12 in the N-terminus of L-PYK.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, MS 3030, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyruvate kinaseA, B, C, D543Homo sapiensMutation(s): 1 
Gene Names: PKLRPK1PKL
EC: 2.7.1.40
UniProt & NIH Common Fund Data Resources
Find proteins for P30613 (Homo sapiens)
Explore P30613 
Go to UniProtKB:  P30613
PHAROS:  P30613
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FBP (Subject of Investigation/LOI)
Query on FBP

Download Ideal Coordinates CCD File 
G [auth A], J [auth B], N [auth C], Q [auth D]1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
 Ligand Interaction
ADN (Subject of Investigation/LOI)
Query on ADN

Download Ideal Coordinates CCD File 
R [auth D]ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
FLC
Query on FLC

Download Ideal Coordinates CCD File 
F [auth A], I [auth B], M [auth C], P [auth D]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
K [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A], H [auth B], L [auth C], O [auth D]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.751α = 90
b = 204.727β = 96.75
c = 86.532γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2013-02-06
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary