5YG8

Crystal structure of ribose-1,5-bisphosphate isomerase from Pyrococcus horikoshii OT3 in complex with ribulose-1,5-bisphosphate, AMP and GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A presumed homologue of the regulatory subunits of eIF2B functions as ribose-1,5-bisphosphate isomerase in Pyrococcus horikoshii OT3.

Gogoi, P.Kanaujia, S.P.

(2018) Sci Rep 8: 1891-1891

  • DOI: 10.1038/s41598-018-20418-w
  • Primary Citation of Related Structures:  5YFJ, 5YFS, 5YFT, 5YFU, 5YFV, 5YFW, 5YFX, 5YG5, 5YG6, 5YG7, 5YG9, 5YGA

  • PubMed Abstract: 
  • The homologues of the regulatory subunits of eukaryotic translation initiation factor 2B (eIF2B) are assumed to be present in archaea. Likewise, an ORF, PH0208 in Pyrococcus horikoshii OT3 have been proposed to encode one of the homologues of regulat ...

    The homologues of the regulatory subunits of eukaryotic translation initiation factor 2B (eIF2B) are assumed to be present in archaea. Likewise, an ORF, PH0208 in Pyrococcus horikoshii OT3 have been proposed to encode one of the homologues of regulatory subunits of eIF2B. However, PH0208 protein also shares sequence similarity with a functionally non-related enzyme, ribose-1,5-bisphosphate isomerase (R15Pi), involved in conversion of ribose-1,5-bisphosphate (R15P) to ribulose-1,5-bisphosphate (RuBP) in an AMP-dependent manner. Herein, we have determined the crystal structure of PH0208 protein in order to decipher its true function. Although structurally similar to the regulatory subunits of eIF2B, the ability to bind R15P and RuBP suggests that PH0208 would function as R15Pi. Additionally, this study for the first time reports the binding sites of AMP and GMP in R15Pi. The AMP binding site in PH0208 protein clarified the role of AMP in providing structural stability to R15Pi. The binding of GMP to the 'AMP binding site' in addition to its own binding site indicates that GMP might also execute a similar function, though with less specificity. Furthermore, we have utilized the resemblance between PH0208 and the regulatory subunits of eIF2B to propose a model for the regulatory mechanism of eIF2B in eukaryotes.


    Organizational Affiliation

    Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribose 1,5-bisphosphate isomerase
A, B, C
324Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)EC: 5.3.1.29
Find proteins for O57947 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O57947
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
RUB
Query on RUB

Download SDF File 
Download CCD File 
A, B, C
RIBULOSE-1,5-DIPHOSPHATE
C5 H12 O11 P2
YAHZABJORDUQGO-NQXXGFSBSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A, B, C
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
G
Query on G

Download SDF File 
Download CCD File 
B, C
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.155 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 98.590α = 90.00
b = 98.590β = 90.00
c = 256.151γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
HKL-3000data collection
MOSFLMdata processing
PHASERphasing
Cootmodel building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Department of Biotechnology (DBT)IndiaBT/302/NE/TBP/2012 dated 07.01.2013

Revision History 

  • Version 1.0: 2018-02-14
    Type: Initial release