3LMI

Crystal Structure of the Inactive Alpha-kinase Domain of Myosin Heavy Chain Kinase A (D766A) complex with ATP

PDB DOI: https://doi.org/10.2210/pdb3LMI/pdb

Classification: TRANSFERASE
Organism(s): Dictyostelium discoideum
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-01-30 Released: 2010-03-16
Deposition Author(s): Ye, Q., Jia, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.269
R-Value Work: 0.199
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of the {alpha}-Kinase Domain of Dictyostelium Myosin Heavy Chain Kinase A.

Ye, Q., Crawley, S.W., Yang, Y., Cote, G.P., Jia, Z.

(2010) Sci Signal 3: ra17-ra17

PubMed: 20197546 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/scisignal.2000525
Primary Citation of Related Structures:
3LKM, 3LLA, 3LMH, 3LMI

PubMed Abstract:
Dictyostelium discoideum myosin II heavy chain kinase A (MHCK A) disrupts the assembly and cellular activity of bipolar filaments of myosin II by phosphorylating sites within its alpha-helical, coiled-coil tail. MHCK A is a member of the atypical alpha-kinase family of serine and threonine protein kinases and displays no sequence homology to typical eukaryotic protein kinases. We report the crystal structure of the alpha-kinase domain (A-CAT) of MHCK A. When crystallized in the presence of adenosine triphosphate (ATP), A-CAT contained adenosine monophosphate (AMP) at the active site. However, when crystallized in the presence of ATP and a peptide substrate, which does not appear in the structure, adenosine diphosphate (ADP) was found at the active site and an invariant aspartic acid residue (Asp(766)) at the active site was phosphorylated. The aspartylphosphate group was exposed to the solvent within an active-site pocket that might function as a docking site for substrates. Access to the aspartylphosphate was regulated by a conformational switch in a loop that bound to a magnesium ion (Mg(2+)), providing a mechanism that allows alpha-kinases to sense and respond to local changes in Mg(2+).

Organizational Affiliation

Department of Biochemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6.

Macromolecule Content

Total Structure Weight: 140.89 kDa
Atom Count: 8,689
Modelled Residue Count: 1,003
Deposited Residue Count: 1,228
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myosin heavy chain kinase A	A, B, C, D	307	Dictyostelium discoideum	Mutation(s): 1 Gene Names: DDB_G0291231, mhckA, mhkA EC: 2.7.11.7
UniProt
Find proteins for P42527 (Dictyostelium discoideum) Explore P42527 Go to UniProtKB: P42527
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42527
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D]	H [auth A], M [auth B], Q [auth C], V [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain V [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth C] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain R [auth D] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D]	E [auth A] I [auth B] J [auth B] N [auth C] R [auth D] E [auth A], I [auth B], J [auth B], N [auth C], R [auth D], S [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain S [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain T [auth D] MOL2 format, chain O [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain T [auth D]	F [auth A], K [auth B], O [auth C], T [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain U [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D]	G [auth A], L [auth B], P [auth C], U [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain U [auth D]