title: Homology models for the PERB11 multigene family.
abstract: BACKGROUND
  PERB11 is a multicopy polymorphic gene family found in association with HLA Class I genes within the major histocompatibility complex (MHC). Although its function is unknown, PERB11 has sequence similarities to HLA Class I and other related proteins. To explore the possible functional roles for PERB11, homology models have been constructed using both HLA Class I and Class I-like protein structures as templates.
  
  
  RESULTS
  The models show that PERB11.1 appears to have an unusual distribution of charged residues that potentially give the molecule a distinct polarity. Furthermore, a cluster of negatively charged residues in the traditional P2 site may form a novel binding site for a positively charged ligand such as a metal ion or complex. Other charged residues line the floor and walls of the cleft and are able to form salt bridges, reminiscent of the closed cleft of the Class I-like mouse neonatal Fc receptor structure. The closely related PERB11.2 family has a different arrangement of charged residues in the cleft, but these residues are still able to form salt bridges. Unlike HLA Class I, the majority of polymorphic positions in the PERB11 family occur outside the cleft and on the surface of the molecule.
  
  
  CONCLUSIONS
  Homology models for PERB11 suggest that the structure is capable of associating with beta2 microglobulin or a similar molecule. Furthermore, not all of the potential glycosylation sites suggested by the PERB11 sequences appear viable. Importantly, the models suggest that the molecule has a less accessible cleft than HLA Class I and is not, therefore, able to bind peptides. Other small ligands, including metal ions, might be bound, however.
authors.affiliation: Human Genetics Group, John Curtin School of Medical Research, Australian National University, Canberra. gareth.chelva@anu.edu.au
authors.forename: G
authors.initials: G
authors.lastname: Chelvanayagam
authors.forename: A
authors.initials: A
authors.lastname: Monaco
authors.forename: J P
authors.initials: JP
authors.lastname: Lalonde
authors.forename: G K
authors.initials: GK
authors.lastname: Tay
authors.forename: R L
authors.initials: RL
authors.lastname: Dawkins
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D005069:Evaluation Studies as Topic; D006031:Glycosylation; D015395:Histocompatibility Antigens Class I / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D008670:Metals / Q000378:metabolism; D008956:Models, Chemical; D008969:Molecular Sequence Data; D005810:Multigene Family; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated; D017386:Sequence Homology, Amino Acid; D001613:beta 2-Microglobulin / Q000378:metabolism
chemical_list: C089801:HCG9 non-protein coding RNA, human; D015395:Histocompatibility Antigens Class I; C099187:MHC class I-related chain A; C098080:MICB antigen; D008670:Metals; D011506:Proteins; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated; D001613:beta 2-Microglobulin