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PDBsum entry 1l7e

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1l7e
Jmol
Contents
Protein chains
372 a.a. *
353 a.a. *
Ligands
NAI ×2
Waters ×607
* Residue conservation analysis
PDB id:
1l7e
Name: Oxidoreductase
Title: Crystal structure of r. Rubrum transhydrogenase domain i with bound nadh
Structure: Nicotinamide nucleotide transhydrogenase, subunit alpha 1. Chain: a, b, c, d. Synonym: transhydrogenase domain i. Engineered: yes
Source: Rhodospirillum rubrum. Organism_taxid: 1085. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.251     R-free:   0.282
Authors: G.S.Prasad,M.Wahlberg,V.Sridhar,M.Yamaguchi,Y.Hatefi, C.D.Stout
Key ref:
G.S.Prasad et al. (2002). Crystal structures of transhydrogenase domain I with and without bound NADH. Biochemistry, 41, 12745-12754. PubMed id: 12379117 DOI: 10.1021/bi020251f
Date:
14-Mar-02     Release date:   20-Nov-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q2RSB2  (PNTAA_RHORT) -  NAD(P) transhydrogenase subunit alpha part 1
Seq:
Struc:
384 a.a.
372 a.a.
Protein chains
Pfam   ArchSchema ?
Q2RSB2  (PNTAA_RHORT) -  NAD(P) transhydrogenase subunit alpha part 1
Seq:
Struc:
384 a.a.
353 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.1.6.1.2  - NAD(P)(+) transhydrogenase (Re/Si-specific).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NADPH + NAD+ = NADP+ + NADH
NADPH
+
NAD(+)
Bound ligand (Het Group name = NAI)
corresponds exactly
= NADP(+)
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     nucleotide binding     10 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi020251f Biochemistry 41:12745-12754 (2002)
PubMed id: 12379117  
 
 
Crystal structures of transhydrogenase domain I with and without bound NADH.
G.S.Prasad, M.Wahlberg, V.Sridhar, V.Sundaresan, M.Yamaguchi, Y.Hatefi, C.D.Stout.
 
  ABSTRACT  
 
Transhydrogenase (TH) is a dimeric integral membrane enzyme in mitochondria and prokaryotes that couples proton translocation across a membrane with hydride transfer between NAD(H) and NADP(H) in soluble domains. Crystal structures of the NAD(H) binding alpha1 subunit (domain I) of Rhodospirillum rubrum TH have been determined at 1.8 A resolution in the absence of dinucleotide and at 1.9 A resolution with NADH bound. Each structure contains two domain I dimers in the asymmetric unit (AB and CD); the dimers are intimately associated and related by noncrystallographic 2-fold axes. NADH binds to subunits A and D, consistent with the half-of-the-sites reactivity of the enzyme. The conformation of NADH in subunits A and D is very similar; the nicotinamide is in the anti conformation, the A-face is exposed to solvent, and both N7 and O7 participate in hydrogen bonds. Comparison of subunits A and D to six independent copies of the subunit without bound NADH reveals multiple conformations for residues and loops surrounding the NADH site, indicating flexibility for binding and release of the substrate (product). The NADH-bound structure is also compared to the structures of R. rubrum domain I with NAD bound (PDB code 1F8G) and with NAD bound in complex with domain III of TH (PDB code 1HZZ). The NADH- vs NAD-bound domain I structures reveal conformational differences in conserved residues in the NAD(H) binding site and in dinucleotide conformation that are correlated with the net charge, i.e., oxidation state, of the nicotinamides. The comparisons illustrate how nicotinamide oxidation state can affect the domain I conformation, which is relevant to the hydride transfer step of the overall reaction.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20513431 K.J.McLaughlin, C.M.Strain-Damerell, K.Xie, D.Brekasis, A.S.Soares, M.S.Paget, and C.L.Kielkopf (2010).
Structural basis for NADH/NAD+ redox sensing by a Rex family repressor.
  Mol Cell, 38, 563-575.
PDB codes: 3ikt 3ikv 3il2
18972197 A.Pedersen, G.B.Karlsson, and J.Rydström (2008).
Proton-translocating transhydrogenase: an update of unsolved and controversial issues.
  J Bioenerg Biomembr, 40, 463-473.  
17911104 U.M.Obiozo, T.H.Brondijk, A.J.White, G.van Boxel, T.R.Dafforn, S.A.White, and J.B.Jackson (2007).
Substitution of tyrosine 146 in the dI component of proton-translocating transhydrogenase leads to reversible dissociation of the active dimer into inactive monomers.
  J Biol Chem, 282, 36434-36443.  
16533815 T.H.Brondijk, G.I.van Boxel, O.C.Mather, P.G.Quirk, S.A.White, and J.B.Jackson (2006).
The role of invariant amino acid residues at the hydride transfer site of proton-translocating transhydrogenase.
  J Biol Chem, 281, 13345-13354.
PDB codes: 2fr8 2frd 2fsv
15039572 C.Oswald, T.Johansson, S.Törnroth, M.Okvist, and U.Krengel (2004).
Crystallization and preliminary crystallographic analysis of the NAD(H)-binding domain of Escherichia coli transhydrogenase.
  Acta Crystallogr D Biol Crystallogr, 60, 743-745.  
12791694 A.Singh, J.D.Venning, P.G.Quirk, G.I.van Boxel, D.J.Rodrigues, S.A.White, and J.B.Jackson (2003).
Interactions between transhydrogenase and thio-nicotinamide Analogues of NAD(H) and NADP(H) underline the importance of nucleotide conformational changes in coupling to proton translocation.
  J Biol Chem, 278, 33208-33216.
PDB codes: 1pt9 1ptj
12972415 J.Broos, E.Gabellieri, G.I.van Boxel, J.B.Jackson, and G.B.Strambini (2003).
Tryptophan phosphorescence spectroscopy reveals that a domain in the NAD(H)-binding component (dI) of transhydrogenase from Rhodospirillum rubrum has an extremely rigid and conformationally homogeneous protein core.
  J Biol Chem, 278, 47578-47584.  
12952962 M.Yamaguchi, and C.D.Stout (2003).
Essential glycine in the proton channel of Escherichia coli transhydrogenase.
  J Biol Chem, 278, 45333-45339.  
14567675 V.Sundaresan, M.Yamaguchi, J.Chartron, and C.D.Stout (2003).
Conformational change in the NADP(H) binding domain of transhydrogenase defines four states.
  Biochemistry, 42, 12143-12153.
PDB codes: 1pno 1pnq
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.