4NJE | pdb_00004nje

Crystal structure of Pyrococcus furiosus L-asparaginase with ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.270 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4NJE

This is version 1.3 of the entry. See complete history

Literature

Structural and functional insights into an archaeal L-asparaginase obtained through the linker-less assembly of constituent domains.

Tomar, R.Sharma, P.Srivastava, A.Bansal, S.Kundu, B.

(2014) Acta Crystallogr D Biol Crystallogr 70: 3187-3197

  • DOI: https://doi.org/10.1107/S1399004714023414
  • Primary Citation Related Structures: 
    4NJE, 4Q0M, 4RA6, 4RA9

  • PubMed Abstract: 

    Covalent linkers bridging the domains of multidomain proteins are considered to be crucial for assembly and function. In this report, an exception in which the linker of a two-domain dimeric L-asparaginase from Pyrococcus furiosus (PfA) was found to be dispensable is presented. Domains of this enzyme assembled without the linker into a conjoined tetrameric form that exhibited higher activity than the parent enzyme. The global shape and quaternary structure of the conjoined PfA were also similar to the wild-type PfA, as observed by their solution scattering profiles and X-ray crystallographic data. Comparison of the crystal structures of substrate-bound and unbound enzymes revealed an altogether new active-site composition and mechanism of action. Thus, conjoined PfA is presented as a unique enzyme obtained through noncovalent, linker-less assembly of constituent domains that is stable enough to function efficiently at elevated temperatures.


  • Organizational Affiliation
    • Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India.

Macromolecule Content 

  • Total Structure Weight: 38.47 kDa 
  • Atom Count: 2,422 
  • Modeled Residue Count: 309 
  • Deposited Residue Count: 351 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
L-asparaginase204Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: ph0066PF2047
EC: 3.5.1.1
UniProt
Find proteins for Q8TZE8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8TZE8 
Go to UniProtKB:  Q8TZE8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TZE8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
L-asparaginase147Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: ph0066PF2047
EC: 3.5.1.1
UniProt
Find proteins for Q8TZE8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8TZE8 
Go to UniProtKB:  Q8TZE8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TZE8
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ASP

Query on ASP



Download:Ideal Coordinates CCD File
C [auth A]ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.270 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.59α = 90
b = 91.59β = 90
c = 188.77γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASESphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary