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PDBsum entry 3b5j

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protein ligands links
Transport protein PDB id
3b5j
Jmol
Contents
Protein chain
243 a.a. *
Ligands
12D
Waters ×261
* Residue conservation analysis
PDB id:
3b5j
Name: Transport protein
Title: Crystal structures of the s504a mutant of an isolated abc-at complex with tnp-adp
Structure: Alpha-hemolysin translocation atp-binding protein chain: a. Fragment: abc transporter, residues unp 467-707. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: hlyb. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Resolution:
2.00Å     R-factor:   0.209     R-free:   0.280
Authors: C.Oswald,S.Jenewein,S.H.J.Smits,I.B.Holland,L.Schmitt
Key ref: C.Oswald et al. (2008). Water-mediated protein-fluorophore interactions modulate the affinity of an ABC-ATPase/TNP-ADP complex. J Struct Biol, 162, 85-93. PubMed id: 18155559 DOI: 10.1016/j.jsb.2007.11.006
Date:
26-Oct-07     Release date:   15-Jan-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P08716  (HLYBP_ECOLX) -  Alpha-hemolysin translocation ATP-binding protein HlyB
Seq:
Struc:
 
Seq:
Struc:
707 a.a.
243 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleotide binding     4 terms  

 

 
DOI no: 10.1016/j.jsb.2007.11.006 J Struct Biol 162:85-93 (2008)
PubMed id: 18155559  
 
 
Water-mediated protein-fluorophore interactions modulate the affinity of an ABC-ATPase/TNP-ADP complex.
C.Oswald, S.Jenewein, S.H.Smits, I.B.Holland, L.Schmitt.
 
  ABSTRACT  
 
TNP-modified nucleotides have been used extensively to study protein-nucleotide interactions. In the case of ABC-ATPases, application of these powerful tools has been greatly restricted due to the significantly higher affinity of the TNP-nucleotide for the corresponding ABC-ATPase in comparison to the non-modified nucleotides. To understand the molecular changes occurring upon binding of the TNP-nucleotide to an ABC-ATPase, we have determined the crystal structure of the TNP-ADP/HlyB-NBD complex at 1.6A resolution. Despite the higher affinity of TNP-ADP, no direct fluorophore-protein interactions were observed. Unexpectedly, only water-mediated interactions were detected between the TNP moiety and Tyr(477), that is engaged in pi-pi stacking with the adenine ring, as well as with two serine residues (Ser(504) and Ser(509)) of the Walker A motif. Interestingly, the side chains of these two serine residues adopt novel conformations that are not observed in the corresponding ADP structure. However, in the crystal structure of the S504A mutant, which binds TNP-ADP with similar affinity to the wild type enzyme, a novel TNP-water interaction compensates for the missing serine side chain. Since this water molecule is not present in the wild type enzyme, these results suggest that only water-mediated interactions provide a structural explanation for the increased affinity of TNP-nucleotides towards ABC-ATPases. However, our results also imply that in silico approaches such as docking or modeling cannot directly be applied to generate 'affinity-adopted' ADP- or ATP-analogs for ABC-ATPases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21239683 C.Toyoshima, S.Yonekura, J.Tsueda, and S.Iwasawa (2011).
Trinitrophenyl derivatives bind differently from parent adenine nucleotides to Ca2+-ATPase in the absence of Ca2+.
  Proc Natl Acad Sci U S A, 108, 1833-1838.
PDB codes: 3ar2 3ar3 3ar4 3ar5 3ar6 3ar7 3ar8 3ar9
20823549 M.Haffke, A.Menzel, Y.Carius, D.Jahn, and D.W.Heinz (2010).
Structures of the nucleotide-binding domain of the human ABCB6 transporter and its complexes with nucleotides.
  Acta Crystallogr D Biol Crystallogr, 66, 979-987.
PDB codes: 3nh6 3nh9 3nha 3nhb
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.