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PDBsum entry 1dm5

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protein metals Protein-protein interface(s) links
Unknown function PDB id
1dm5
Jmol
Contents
Protein chains
(+ 0 more) 315 a.a. *
Metals
_CA ×11
Waters ×926
* Residue conservation analysis
PDB id:
1dm5
Name: Unknown function
Title: Annexin xii e105k homohexamer crystal structure
Structure: Annexin xii e105k mutant homohexamer. Chain: a, b, c, d, e, f. Engineered: yes. Mutation: yes
Source: Hydra vulgaris. Organism_taxid: 6087. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
Resolution:
1.93Å     R-factor:   0.236     R-free:   0.263
Authors: J.P.Cartailler,H.T.Haigler,H.Luecke
Key ref:
J.P.Cartailler et al. (2000). Annexin XII E105K crystal structure: identification of a pH-dependent switch for mutant hexamerization. Biochemistry, 39, 2475-2483. PubMed id: 10704197 DOI: 10.1021/bi992278d
Date:
13-Dec-99     Release date:   20-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P26256  (ANX12_HYDVU) -  Annexin-B12
Seq:
Struc:
316 a.a.
315 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     calcium-dependent phospholipid binding     2 terms  

 

 
DOI no: 10.1021/bi992278d Biochemistry 39:2475-2483 (2000)
PubMed id: 10704197  
 
 
Annexin XII E105K crystal structure: identification of a pH-dependent switch for mutant hexamerization.
J.P.Cartailler, H.T.Haigler, H.Luecke.
 
  ABSTRACT  
 
Annexins are a family of calcium- and phospholipid-binding proteins involved with numerous cellular processes including membrane fusion, ion channel activity, and heterocomplex formation with other proteins. The annexin XII (ANXB12) crystal structure presented evidence that calcium mediates the formation of a hexamer through a novel intermolecular calcium-binding site [Luecke et al. (1995) Nature 378, 512-515]. In an attempt to disrupt hexamerization, we mutated a conserved key ligand in the intermolecular calcium-binding site, Glu105, to lysine. Despite its occurrence in a new spacegroup, the 1.93 A resolution structure reveals a hexamer with the Lys105 epsilon-amino group nearly superimposable with the original intermolecular calcium position. Our analysis shows that the mutation is directly involved in stabilizing the hexamer. The local residues are reoriented to retain affinity between the two trimers via a pH-dependent switch residue, Glu76, which is now protonated, allowing it to form tandem hydrogen bonds with the backbone carbonyl and nitrogen atoms of Thr103 located across the trimer interface. The loss of the intermolecular calcium-binding site is recuperated by extensive hydrogen bonding favoring hexamer stabilization. The presence of this mutant structure provides further evidence for hexameric annexin XII, and possible in vivo roles are discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19888325 C.Tortiglione, A.Quarta, M.A.Malvindi, A.Tino, and T.Pellegrino (2009).
Fluorescent nanocrystals reveal regulated portals of entry into and between the cells of Hydra.
  PLoS One, 4, e7698.  
18212017 T.E.Williamson, B.A.Craig, E.Kondrashkina, C.Bailey-Kellogg, and A.M.Friedman (2008).
Analysis of self-associating proteins by singular value decomposition of solution scattering data.
  Biophys J, 94, 4906-4923.  
17452342 K.M.Gorecka, C.Thouverey, R.Buchet, and S.Pikula (2007).
Potential role of annexin AnnAt1 from Arabidopsis thaliana in pH-mediated cellular response to environmental stimuli.
  Plant Cell Physiol, 48, 792-803.  
15298924 M.Golczak, A.Kirilenko, J.Bandorowicz-Pikula, B.Desbat, and S.Pikula (2004).
Structure of human annexin a6 at the air-water interface and in a membrane-bound state.
  Biophys J, 87, 1215-1226.  
11964259 A.Kirilenko, M.Golczak, S.Pikula, R.Buchet, and J.Bandorowicz-Pikula (2002).
GTP-induced membrane binding and ion channel activity of annexin VI: is annexin VI a GTP biosensor?
  Biophys J, 82, 2737-2745.  
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.