[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

TitleStructural characterization of NrnC identifies unifying features of dinucleotidases.
Journal, issue, pagesElife, Vol. 10, Year 2021
Publish dateSep 17, 2021
AuthorsJustin D Lormand / Soo-Kyoung Kim / George A Walters-Marrah / Bryce A Brownfield / J Christopher Fromme / Wade C Winkler / Jonathan R Goodson / Vincent T Lee / Holger Sondermann /
PubMed AbstractRNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. ...RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process. We recently showed that oligoribonuclease (Orn) acts as a dedicated diribonucleotidase, defining the ultimate step in RNA degradation that is crucial for cellular fitness (Kim et al., 2019). Whether such a specific activity exists in organisms that lack Orn-type exoribonucleases remained unclear. Through quantitative structure-function analyses, we show here that NrnC-type RNases share this narrow substrate length preference with Orn. Although NrnC and Orn employ similar structural features that distinguish these two classes of dinucleotidases from other exonucleases, the key determinants for dinucleotidase activity are realized through distinct structural scaffolds. The structures, together with comparative genomic analyses of the phylogeny of DEDD-type exoribonucleases, indicate convergent evolution as the mechanism of how dinucleotidase activity emerged repeatedly in various organisms. The evolutionary pressure to maintain dinucleotidase activity further underlines the important role these analogous proteins play for cell growth.
External linksElife / PubMed:34533457 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.42 - 3.69 Å
Structure data

EMDB-23941, PDB-7mqb:
Bartonella henselae NrnC bound to pGG. D4 Symmetry
Method: EM (single particle) / Resolution: 3.25 Å

EMDB-23942, PDB-7mqc:
Bartonella henselae NrnC bound to pGG. C1 reconstruction.
Method: EM (single particle) / Resolution: 3.64 Å

EMDB-23943, PDB-7mqd:
Bartonella henselae NrnC complexed with pAGG. D4 symmetry.
Method: EM (single particle) / Resolution: 3.25 Å

EMDB-23944, PDB-7mqe:
Bartonella henselae NrnC complexed with pAGG. C1 reconstruction.
Method: EM (single particle) / Resolution: 3.69 Å

EMDB-23945, PDB-7mqf:
Bartonella henselae NrnC complexed with pAAAGG. D4 symmetry.
Method: EM (single particle) / Resolution: 2.88 Å

EMDB-23946, PDB-7mqg:
Bartonella henselae NrnC complexed with pAAAGG. C1 reconstruction.
Method: EM (single particle) / Resolution: 3.25 Å

EMDB-23947, PDB-7mqh:
Bartonella henselae NrnC complexed with pAAAGG in the presence of Ca2+. D4 Symmetry.
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-23948, PDB-7mqi:
Bartonella henselae NrnC complexed with pAAAGG in the presence of Ca2+. C1 reconstruction.
Method: EM (single particle) / Resolution: 3.21 Å

PDB-7mpl:
Bartonella henselae NrnC bound to pGG
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7mpm:
Bartonella henselae NrnC bound to pAA
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-7mpn:
Bartonella henselae NrnC bound to pGC
Method: X-RAY DIFFRACTION / Resolution: 1.94 Å

PDB-7mpo:
Bartonella henselae NrnC bound to pAp
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-7mpp:
Bartonella henselae NrnC cleaving pGG in the presence of Mg2+
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-7mpq:
Bartonella henselae NrnC cleaving pGG in the presence of Mn2+
Method: X-RAY DIFFRACTION / Resolution: 2.35 Å

PDB-7mpr:
Brucella melitensis NrnC
Method: X-RAY DIFFRACTION / Resolution: 1.42 Å

PDB-7mps:
Brucella melitensis NrnC with engaged loop
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-7mpt:
Brucella melitensis NrnC with bound Mg2+
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-7mpu:
Brucella melitensis NrnC bound to pGG
Method: X-RAY DIFFRACTION / Resolution: 1.72 Å

Chemicals

ChemComp-HOH:
WATER

ChemComp-A3P:
ADENOSINE-3'-5'-DIPHOSPHATE

ChemComp-5GP:
GUANOSINE-5'-MONOPHOSPHATE

ChemComp-MG:
Unknown entry

ChemComp-MN:
Unknown entry

ChemComp-SO4:
SULFATE ION

ChemComp-EPE:
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH buffer*YM

ChemComp-PO4:
PHOSPHATE ION

Source
  • bartonella henselae (bacteria)
  • synthetic construct (others)
  • brucella melitensis (bacteria)
KeywordsRNA BINDING PROTEIN/RNA / RNase / bacteria / enzyme / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA 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