2OOY

Crystal structure of the adenylate sensor from AMP-activated protein kinase complexed with ATP

PDB DOI: https://doi.org/10.2210/pdb2OOY/pdb

Classification: TRANSFERASE
Organism(s): Schizosaccharomyces pombe
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-01-26 Released: 2007-02-06
Deposition Author(s): Townley, R., Shapiro, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free: 0.298
R-Value Work: 0.189
R-Value Observed: 0.195

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structures of the adenylate sensor from fission yeast AMP-activated protein kinase.

Townley, R., Shapiro, L.

(2007) Science 315: 1726-1729

PubMed: 17289942 Search on PubMed
DOI: https://doi.org/10.1126/science.1137503
Primary Citation of Related Structures:
2OOX, 2OOY

PubMed Abstract:
The 5'-AMP (adenosine monophosphate)-activated protein kinase (AMPK) coordinates metabolic function with energy availability by responding to changes in intracellular ATP (adenosine triphosphate) and AMP concentrations. Here, we report crystal structures at 2.9 and 2.6 A resolution for ATP- and AMP-bound forms of a core alphabetagamma adenylate-binding domain from the fission yeast AMPK homolog. ATP and AMP bind competitively to a single site in the gamma subunit, with their respective phosphate groups positioned near function-impairing mutants. Unexpectedly, ATP binds without counterions, amplifying its electrostatic effects on a critical regulatory region where all three subunits converge.

Organizational Affiliation

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.

Macromolecule Content

Total Structure Weight: 129.47 kDa
Atom Count: 9,010
Modelled Residue Count: 1,084
Deposited Residue Count: 1,134
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SNF1-like protein kinase ssp2	A, D [auth C]	137	Schizosaccharomyces pombe	Mutation(s): 0 Gene Names: ssp2, SPCC74.03c EC: 2.7.11.1
UniProt
Find proteins for O74536 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O74536 Go to UniProtKB: O74536
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O74536
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SPCC1919.03c protein	B, E [auth D]	97	Schizosaccharomyces pombe	Mutation(s): 0 Gene Names: SPCC1919.03c
UniProt
Find proteins for P78789 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P78789 Go to UniProtKB: P78789
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P78789
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein C1556.08c in chromosome I	C [auth G], F [auth E]	333	Schizosaccharomyces pombe	Mutation(s): 0 Gene Names: SPAC1556.08c, SPAC1F12.01c
UniProt
Find proteins for Q10343 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q10343 Go to UniProtKB: Q10343
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q10343
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain G SDF format, chain I [auth E] MOL2 format, chain G MOL2 format, chain I [auth E] mmCIF format, chain G mmCIF format, chain I [auth E]	G, I [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain G Focus chain I [auth E] Interactions & Density Focus chain G Focus chain I [auth E]
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain H [auth E] MOL2 format, chain H [auth E] mmCIF format, chain H [auth E]	H [auth E]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain H [auth E] Interactions & Density Focus chain H [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free: 0.298
R-Value Work: 0.189
R-Value Observed: 0.195
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.902	α = 90
b = 77.666	β = 123.99
c = 107.576	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-02-06

Deposition Author(s):

Townley, R.

Shapiro, L.

Revision History (Full details and data files)

Version 1.0: 2007-02-06
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-30
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description