1E3T | pdb_00001e3t

Solution Structure of the NADP(H) binding Component (dIII) of Proton-Translocating Transhydrogenase from Rhodospirillum rubrum


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 
  • Selection Criteria: AVERAGE OF 10 LOWEST ENERGY STRUCTURES 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Solution Structure of the Nadp(H)-Binding Component (Diii) of Proton-Translocating Transhydrogenase from Rhodospirillum Rubrum

Jeeves, M.Smith, K.J.Quirk, P.G.Cotton, N.P.J.Jackson, J.B.

(2000) Biochim Biophys Acta 1459: 248

  • DOI: https://doi.org/10.1016/s0005-2728(00)00159-6
  • Primary Citation Related Structures: 
    1E3T

  • PubMed Abstract: 

    Transhydrogenase is a proton pump found in the membranes of bacteria and animal mitochondria. The solution structure of the expressed, 21.5 kDa, NADP(H)-binding component (dIII) of transhydrogenase from Rhodospirillum rubrum has been solved by NMR methods. This is the first description of the structure of dIII from a bacterial source. The protein adopts a Rossmann fold: an open, twisted, parallel beta-sheet, flanked by helices. However, the binding of NADP(+) to dIII is profoundly different to that seen in other Rossmann structures, in that its orientation is reversed: the adenosine moiety interacts with the first betaalphabetaalphabeta motif, and the nicotinamide with the second. Features in the structure that might be responsible for changes in nucleotide-binding affinity during catalysis, and for interaction with other components of the enzyme, are identified. The results are compared with the recently determined, high-resolution crystal structures of human and bovine dIII which also show the reversed nucleotide orientation.


  • Organizational Affiliation
    • School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK.

Macromolecule Content 

  • Total Structure Weight: 22.23 kDa 
  • Atom Count: 1,370 
  • Modeled Residue Count: 175 
  • Deposited Residue Count: 203 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE (SUBUNIT BETA)203Rhodospirillum rubrumMutation(s): 0 
Gene Names: PNTB
EC: 1.6.1.1 (PDB Primary Data), 7.1.1.1 (UniProt)
UniProt
Find proteins for Q2RSB4 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1))
Explore Q2RSB4 
Go to UniProtKB:  Q2RSB4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2RSB4
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on NAP



Download:Ideal Coordinates CCD File
B [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 
  • Selection Criteria: AVERAGE OF 10 LOWEST ENERGY STRUCTURES 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-10-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references, Derived calculations