5FH4

The structure of rat cytosolic PEPCK variant E89D in complex with beta-sulfopyruvate and GTP

  • Classification: LYASE
  • Organism(s): Rattus norvegicus
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2015-12-21 Released: 2016-11-09 
  • Deposition Author(s): Johnson, T.A., Holyoak, T.
  • Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR), Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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Literature

Utilization of Substrate Intrinsic Binding Energy for Conformational Change and Catalytic Function in Phosphoenolpyruvate Carboxykinase.

Johnson, T.A., Mcleod, M.J., Holyoak, T.

(2016) Biochemistry 55: 575-587

  • DOI: 10.1021/acs.biochem.5b01215
  • Primary Citation of Related Structures:  
    5FH0, 5FH1, 5FH2, 5FH3, 5FH4, 5FH5

  • PubMed Abstract: 

    • Phosphoenolpyruvate carboxykinase (PEPCK) is an essential metabolic enzyme operating in the gluconeogenesis and glyceroneogenesis pathways. Previous work has demonstrated that the enzyme cycles between a catalytically inactive open state and a catalytically active closed state ...

    Phosphoenolpyruvate carboxykinase (PEPCK) is an essential metabolic enzyme operating in the gluconeogenesis and glyceroneogenesis pathways. Previous work has demonstrated that the enzyme cycles between a catalytically inactive open state and a catalytically active closed state. The transition of the enzyme between these states requires the transition of several active site loops to shift from mobile, disordered structural elements to stable ordered states. The mechanism by which these disorder-order transitions are coupled to the ligation state of the active site however is not fully understood. To further investigate the mechanisms by which the mobility of the active site loops is coupled to enzymatic function and the transitioning of the enzyme between the two conformational states, we have conducted structural and functional studies of point mutants of E89. E89 is a proposed key member of the interaction network of mobile elements as it resides in the R-loop region of the enzyme active site. These new data demonstrate the importance of the R-loop in coordinating interactions between substrates at the OAA/PEP binding site and the mobile R- and Ω-loop domains. In turn, the studies more generally demonstrate the mechanisms by which the intrinsic ligand binding energy can be utilized in catalysis to drive unfavorable conformational changes, changes that are subsequently required for both optimal catalytic activity and fidelity.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center , Kansas City, Kansas 66160, United States.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphoenolpyruvate carboxykinase, cytosolic [GTP]A622Rattus norvegicusMutation(s): 1 
Gene Names: Pck1
EC: 4.1.1.32 (PDB Primary Data), 2.7.11 (UniProt)
UniProt
Find proteins for P07379 (Rattus norvegicus)
Explore P07379 
Go to UniProtKB:  P07379
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07379
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
E [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
SPV
Query on SPV
Download Ideal Coordinates CCD File 
F [auth A]SULFOPYRUVATE
C3 H4 O6 S
BUTHMSUEBYPMKJ-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
MN
Query on MN
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
I [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SPV BindingDB:  5FH4 Ki: 3.70e+4 (nM) from 1 assay(s)
Binding MOAD:  5FH4 Ki: 1.74e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.59α = 90
b = 118.809β = 109.3
c = 60.508γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesP20 RR17708
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence