PDBsum entry 6z3a

Hydrolase

PDB id: 6z3a

Contents

Protein chains

2311 a.a.

554 a.a.

Ligands

ANP ×2

Metals

_ZN ×2

PDB id:

6z3a

Name:

Hydrolase

Title:

Mec1-ddc2 (wild-type) in complex with amp-pnp

Structure:

Serine/threonine-protein kinase mec1. Chain: f, e. Synonym: atr homolog,DNA-damage checkpoint kinase mec1,mitosis entry checkpoint protein 1. Engineered: yes. DNA damage checkpoint protein lcd1. Chain: c, d. Synonym: DNA damage checkpoint protein 2,lethal,checkpoint-defective, DNA damage-sensitive protein 1.

Source:

Saccharomyces cerevisiae s288c. Organism_taxid: 559292. Gene: mec1, esr1, sad3, ybr136w, ybr1012. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932. Expression_system_variant: py252. Gene: lcd1, ddc2, pie1, ydr499w.

Authors:

L.A.Yates,X.Zhang

Key ref:

E.A.Tannous et al. (2021). Mechanism of auto-inhibition and activation of Mec1^ATR checkpoint kinase. Nat Struct Mol Biol, 28, 50-61. PubMed id: 33169019 DOI: 10.1016/j.jsb.2012.09.006

Date:

19-May-20 Release date: 11-Nov-20

Protein chains

P38111  (ATR_YEAST) -  Serine/threonine-protein kinase MEC1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 2368 a.a.

Struc: 2311 a.a.

Protein chains

Q04377  (LCD1_YEAST) -  DNA damage checkpoint protein LCD1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 747 a.a.

Struc: 554 a.a.

Enzyme reactions

• Enzyme class 2: Chains C, D: E.C.?
• Enzyme class 3: Chains F, E: E.C.2.7.11.1 - non-specific serine/threonine protein kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] (Bound ligand (Het Group name = ANP) matches with 81.25% similarity) + ADP + H(+)

L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] (Bound ligand (Het Group name = ANP) matches with 81.25% similarity) + ADP + H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jsb.2012.09.006

Nat Struct Mol Biol 28:50-61 (2021)

PubMed id: 33169019

Mechanism of auto-inhibition and activation of Mec1^ATR checkpoint kinase.

E.A.Tannous, L.A.Yates, X.Zhang, P.M.Burgers.

ABSTRACT

In response to DNA damage or replication fork stalling, the basal activity of Mec1^ATR is stimulated in a cell-cycle-dependent manner, leading to cell-cycle arrest and the promotion of DNA repair. Mec1^ATR dysfunction leads to cell death in yeast and causes chromosome instability and embryonic lethality in mammals. Thus, ATR is a major target for cancer therapies in homologous recombination-deficient cancers. Here we identify a single mutation in Mec1, conserved in ATR, that results in constitutive activity. Using cryo-electron microscopy, we determine the structures of this constitutively active form (Mec1(F2244L)-Ddc2) at 2.8 Å and the wild type at 3.8 Å, both in complex with Mg²⁺-AMP-PNP. These structures yield a near-complete atomic model for Mec1-Ddc2 and uncover the molecular basis for low basal activity and the conformational changes required for activation. Combined with biochemical and genetic data, we discover key regulatory regions and propose a Mec1 activation mechanism.