3DTB | pdb_00003dtb

The structure of rat cytosolic PEPCK in complex with phosphoglycolate and GDP

PDB DOI: https://doi.org/10.2210/pdb3DTB/pdb

Classification: LYASE
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-14 Released: 2008-08-26
Deposition Author(s): Sullivan, S.M., Holyoak, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.193 (Depositor), 0.193 (DCC)
R-Value Work:
0.168 (Depositor), 0.171 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection.

Sullivan, S.M., Holyoak, T.

(2008) Proc Natl Acad Sci U S A 105: 13829-13834

PubMed: 18772387 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.0805364105
Primary Citation Related Structures:
3DT2, 3DT4, 3DT7, 3DTB

PubMed Abstract:
The induced fit and conformational selection/population shift models are two extreme cases of a continuum aimed at understanding the mechanism by which the final key-lock or active enzyme conformation is achieved upon formation of the correctly ligated enzyme. Structures of complexes representing the Michaelis and enolate intermediate complexes of the reaction catalyzed by phosphoenolpyruvate carboxykinase provide direct structural evidence for the encounter complex that is intrinsic to the induced fit model and not required by the conformational selection model. In addition, the structural data demonstrate that the conformational selection model is not sufficient to explain the correlation between dynamics and catalysis in phosphoenolpyruvate carboxykinase and other enzymes in which the transition between the uninduced and the induced conformations occludes the active site from the solvent. The structural data are consistent with a model in that the energy input from substrate association results in changes in the free energy landscape for the protein, allowing for structural transitions along an induced fit pathway.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.

Macromolecule Content

Total Structure Weight: 141.53 kDa
Atom Count: 11,713
Modeled Residue Count: 1,232
Deposited Residue Count: 1,248
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate carboxykinase, cytosolic [GTP]	A, B	624	Rattus norvegicus	Mutation(s): 0 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07379
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain H [auth A]	H [auth A], P [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain H [auth A] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain P [auth B]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
PGA Query on PGA Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain C [auth A]	C [auth A], L [auth B]	2-PHOSPHOGLYCOLIC ACID C₂ H₅ O₆ P ASCFNMCAHFUBCO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
BCT Query on BCT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], M [auth B], N [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain M [auth B] Focus chain N [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A]	F [auth A], O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.193 (Depositor), 0.193 (DCC)
R-Value Work: 0.168 (Depositor), 0.171 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.154	α = 90
b = 119.683	β = 107.05
c = 86.849	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-08-26

Deposition Author(s):

Sullivan, S.M.

Holyoak, T.

Revision History (Full details and data files)

Version 1.0: 2008-08-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations