Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Tubulin code eraser CCP5 binds branch glutamates by substrate deformation.
Journal, issue, pages	Nature, Vol. 631, Issue 8022, Page 905-912, Year 2024
Publish date	Jul 17, 2024
Authors	Jiayi Chen / Elena A Zehr / James M Gruschus / Agnieszka Szyk / Yanjie Liu / Martin E Tanner / Nico Tjandra / Antonina Roll-Mecak /
PubMed Abstract	Microtubule function is modulated by the tubulin code, diverse posttranslational modifications that are altered dynamically by writer and eraser enzymes. Glutamylation-the addition of branched ...Microtubule function is modulated by the tubulin code, diverse posttranslational modifications that are altered dynamically by writer and eraser enzymes. Glutamylation-the addition of branched (isopeptide-linked) glutamate chains-is the most evolutionarily widespread tubulin modification. It is introduced by tubulin tyrosine ligase-like enzymes and erased by carboxypeptidases of the cytosolic carboxypeptidase (CCP) family. Glutamylation homeostasis, achieved through the balance of writers and erasers, is critical for normal cell function, and mutations in CCPs lead to human disease. Here we report cryo-electron microscopy structures of the glutamylation eraser CCP5 in complex with the microtubule, and X-ray structures in complex with transition-state analogues. Combined with NMR analysis, these analyses show that CCP5 deforms the tubulin main chain into a unique turn that enables lock-and-key recognition of the branch glutamate in a cationic pocket that is unique to CCP family proteins. CCP5 binding of the sequences flanking the branch point primarily through peptide backbone atoms enables processing of diverse tubulin isotypes and non-tubulin substrates. Unexpectedly, CCP5 exhibits inefficient processing of an abundant β-tubulin isotype in the brain. This work provides an atomistic view into glutamate branch recognition and resolution, and sheds light on homeostasis of the tubulin glutamylation syntax.
External links	Nature / PubMed:39020174
Methods	EM (single particle) / X-ray diffraction
Resolution	1.8 - 3.6 Å
Structure data	EMDB-42948: Microtubule protofilament reconstruction in CCP5:microtubule class#1 complex Method: EM (single particle) / Resolution: 3.0 Å 42950 8v3q EMDB-42950, PDB-8v3q: Structure of CCP5 class1 Method: EM (single particle) / Resolution: 3.1 Å 42951 8v3r EMDB-42951, PDB-8v3r: Structure of CCP5 class2 Method: EM (single particle) / Resolution: 3.4 Å 42952 8v3s EMDB-42952, PDB-8v3s: Structure of CCP5 class3 Method: EM (single particle) / Resolution: 3.6 Å 42971 8v4k EMDB-42971, PDB-8v4k: CCP5 in complex with microtubules class1 Method: EM (single particle) / Resolution: 3.1 Å 42972 8v4l EMDB-42972, PDB-8v4l: CCP5 in complex with microtubules class2 Method: EM (single particle) / Resolution: 2.9 Å 42973 8v4m EMDB-42973, PDB-8v4m: CCP5 in complex with microtubules class3 Method: EM (single particle) / Resolution: 3.0 Å EMDB-44544: Microtubule protofilament reconstruction in CCP5:microtubule class#2 complex Method: EM (single particle) / Resolution: 3.1 Å EMDB-44545: Microtubule Protofilament reconstruction in CCP5:microtubule class#3 complex Method: EM (single particle) / Resolution: 3.2 Å PDB-8v3m: CCP5 apo structure Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-8v3n: CCP5 in complex with Glu-P-Glu transition state analog Method: X-RAY DIFFRACTION / Resolution: 2.3 Å PDB-8v3o: CCP5 in complex with Glu-P-peptide 1 transition state analog Method: X-RAY DIFFRACTION / Resolution: 2.3 Å PDB-8v3p: CCP5 in complex with Glu-P-peptide 2 transition state analog Method: X-RAY DIFFRACTION / Resolution: 2.36 Å
Chemicals	ChemComp-MLT: D-MALATE ChemComp-IMD: IMIDAZOLE ChemComp-ZN: Unknown entry ChemComp-HOH: WATER PDB-1aag: Unknown entry ChemComp-K: Unknown entry ChemComp-GLU: GLUTAMIC ACID ChemComp-MG: Unknown entry ChemComp-GTP: GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying moleculeYM ChemComp-G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogueYM
Source	sus scrofa (pig) homo sapiens (human)
Keywords	HYDROLASE / carboxypeptidase deglutamylation branch glutamate removal microtubule / HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR complex / carboxypeptidase / deglutamylation / branch glutamate removal / microtubule / HYDROLASE/SUBSTRATE / HYDROLASE-SUBSTRATE complex / STRUCTURAL PROTEIN / HYDROLASE-SUBSTRATE / STRUCTURAL PROTEIN complex