7MPP

Bartonella henselae NrnC cleaving pGG in the presence of Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural characterization of NrnC identifies unifying features of dinucleotidases.

Lormand, J.D.Kim, S.K.Walters-Marrah, G.A.Brownfield, B.A.Fromme, J.C.Winkler, W.C.Goodson, J.R.Lee, V.T.Sondermann, H.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.70146
  • Primary Citation of Related Structures:  
    7MPL, 7MPM, 7MPN, 7MPO, 7MPP, 7MPQ, 7MPR, 7MPS, 7MPT, 7MPU, 7MQB, 7MQC, 7MQD, 7MQE, 7MQF, 7MQG, 7MQH, 7MQI

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Department of Molecular Medicine, Cornell University, Ithaca, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NanoRNase C207Bartonella henselaeMutation(s): 0 
Gene Names: BM1374165_00260
UniProt
Find proteins for X5MEI1 (Bartonella henselae)
Explore X5MEI1 
Go to UniProtKB:  X5MEI1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupX5MEI1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5GP
Query on 5GP

Download Ideal Coordinates CCD File 
BA [auth I]
CA [auth K]
DA [auth K]
GA [auth M]
HA [auth M]
BA [auth I],
CA [auth K],
DA [auth K],
GA [auth M],
HA [auth M],
I [auth A],
KA [auth O],
L [auth A],
LA [auth O],
M [auth C],
P [auth C],
Q [auth E],
T [auth E],
U [auth G],
V [auth G],
Y [auth I]
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth I]
EA [auth K]
FA [auth K]
IA [auth M]
J [auth A]
AA [auth I],
EA [auth K],
FA [auth K],
IA [auth M],
J [auth A],
JA [auth M],
K [auth A],
MA [auth O],
N [auth C],
NA [auth O],
O [auth C],
R [auth E],
S [auth E],
W [auth G],
X [auth G],
Z [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.929α = 90
b = 126.734β = 94.278
c = 127.145γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
pointlessdata scaling
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI142400

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description