[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

TitleMolecular analysis and essentiality of Aro1 shikimate biosynthesis multi-enzyme in .
Journal, issue, pagesLife Sci Alliance, Vol. 5, Issue 8, Year 2022
Publish dateMay 5, 2022
AuthorsPeter J Stogios / Sean D Liston / Cameron Semper / Bradley Quade / Karolina Michalska / Elena Evdokimova / Shane Ram / Zbyszek Otwinowski / Dominika Borek / Leah E Cowen / Alexei Savchenko /
PubMed AbstractIn the human fungal pathogen , encodes an essential multi-enzyme that catalyses consecutive steps in the shikimate pathway for biosynthesis of chorismate, a precursor to folate and the aromatic ...In the human fungal pathogen , encodes an essential multi-enzyme that catalyses consecutive steps in the shikimate pathway for biosynthesis of chorismate, a precursor to folate and the aromatic amino acids. We obtained the first molecular image of Aro1 that reveals the architecture of all five enzymatic domains and their arrangement in the context of the full-length protein. Aro1 forms a flexible dimer allowing relative autonomy of enzymatic function of the individual domains. Our activity and in cellulo data suggest that only four of Aro1's enzymatic domains are functional and essential for viability of , whereas the 3-dehydroquinate dehydratase (DHQase) domain is inactive because of active site substitutions. We further demonstrate that in , the type II DHQase Dqd1 can compensate for the inactive DHQase domain of Aro1, suggesting an unrecognized essential role for this enzyme in shikimate biosynthesis. In contrast, in and , which do not encode a Dqd1 homolog, Aro1 DHQase domains are enzymatically active, highlighting diversity across species.
External linksLife Sci Alliance / PubMed:35512834 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.85 - 4.16 Å
Structure data

26357

7u5s

EMDB-26357, PDB-7u5s:
CryoEM structure of the Candida albicans Aro1 dimer
Method: EM (single particle) / Resolution: 4.16 Å

26358

7u5t

EMDB-26358, PDB-7u5t:
Structure of DHQS/EPSPS dimer from Candida albicans Aro1
Method: EM (single particle) / Resolution: 3.43 Å

26359

7u5u

EMDB-26359, PDB-7u5u:
Structure of the SK/DHQase/DHSD dimer from Candida albicans Aro1
Method: EM (single particle) / Resolution: 3.16 Å

PDB-6c5c:
Crystal structure of the 3-dehydroquinate synthase (DHQS) domain of Aro1 from Candida albicans SC5314 in complex with NADH
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-7tbu:
Crystal structure of the 5-enolpyruvate-shikimate-3-phosphate synthase (EPSPS) domain of Aro1 from Candida albicans in complex with shikimate-3-phosphate
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-7tbv:
Crystal structure of the shikimate kinase + 3-dehydroquinate dehydratase + 3-dehydroshikimate dehydrogenase domains of Aro1 from Candida albicans
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

Chemicals

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-CL:
Unknown entry / Chloride

ChemComp-HOH:
WATER / Water

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM / Tris

ChemComp-S3P:
SHIKIMATE-3-PHOSPHATE

ChemComp-MG:
Unknown entry

ChemComp-GOL:
GLYCEROL / Glycerol

Source
  • candida albicans (yeast)
  • candida albicans (strain sc5314 / atcc mya-2876) (yeast)
  • candida albicans ca6 (yeast)
KeywordsLYASE / chorismate biosynthesis / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TRANSFERASE / OXIDOREDUCTASE / BIOSYNTHETIC PROTEIN

+
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