[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleTubulin code eraser CCP5 binds branch glutamates by substrate deformation.
Journal, issue, pagesNature, Vol. 631, Issue 8022, Page 905-912, Year 2024
Publish dateJul 17, 2024
AuthorsJiayi Chen / Elena A Zehr / James M Gruschus / Agnieszka Szyk / Yanjie Liu / Martin E Tanner / Nico Tjandra / Antonina Roll-Mecak /
PubMed AbstractMicrotubule 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 linksNature / PubMed:39020174
MethodsEM (single particle) / X-ray diffraction
Resolution1.8 - 3.6 Å
Structure data

EMDB-42948: Microtubule protofilament reconstruction in CCP5:microtubule class#1 complex
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-42950, PDB-8v3q:
Structure of CCP5 class1
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-42951, PDB-8v3r:
Structure of CCP5 class2
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-42952, PDB-8v3s:
Structure of CCP5 class3
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-42971, PDB-8v4k:
CCP5 in complex with microtubules class1
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-42972, PDB-8v4l:
CCP5 in complex with microtubules class2
Method: EM (single particle) / Resolution: 2.9 Å

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 molecule*YM

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

Source
  • sus scrofa (pig)
  • homo sapiens (human)
KeywordsHYDROLASE / 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

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more