spacer
spacer

PDBsum entry 1qxp

Go to PDB code: 
protein Protein-protein interface(s) links
Hydrolase chimera PDB id
1qxp
Jmol
Contents
Protein chains
783 a.a. *
788 a.a. *
Waters ×312
* Residue conservation analysis
PDB id:
1qxp
Name: Hydrolase chimera
Title: Crystal structure of a mu-like calpain
Structure: Mu-like calpain. Chain: a, b. Engineered: yes. Mutation: yes. Other_details: residues 1-49 from m-calpain, residues 60- 647 of mu-calpain, residues 636-700 of m-calpain and residues 83-266 of calcium-activated neutral proteinase.
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.80Å     R-factor:   0.233     R-free:   0.311
Authors: G.P.Pal,T.D.Veyra,J.S.Elce,Z.Jia
Key ref:
G.P.Pal et al. (2003). Crystal structure of a micro-like calpain reveals a partially activated conformation with low Ca2+ requirement. Structure, 11, 1521-1526. PubMed id: 14656436 DOI: 10.1016/j.str.2003.11.007
Date:
08-Sep-03     Release date:   03-Feb-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P97571  (CAN1_RAT) -  Calpain-1 catalytic subunit
Seq:
Struc:
 
Seq:
Struc:
713 a.a.
783 a.a.*
Protein chain
Pfam   ArchSchema ?
Q07009  (CAN2_RAT) -  Calpain-2 catalytic subunit
Seq:
Struc:
 
Seq:
Struc:
700 a.a.
783 a.a.*
Protein chain
Pfam   ArchSchema ?
P97571  (CAN1_RAT) -  Calpain-1 catalytic subunit
Seq:
Struc:
 
Seq:
Struc:
713 a.a.
788 a.a.*
Protein chain
Pfam   ArchSchema ?
Q07009  (CAN2_RAT) -  Calpain-2 catalytic subunit
Seq:
Struc:
 
Seq:
Struc:
700 a.a.
788 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 477 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: Chains A, B: E.C.3.4.22.52  - Calpain-1.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Cofactor: Ca(2+)
   Enzyme class 2: Chains A, B: E.C.3.4.22.53  - Calpain-2.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Cofactor: Ca(2+)
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     proteolysis   1 term 
  Biochemical function     calcium ion binding     2 terms  

 

 
DOI no: 10.1016/j.str.2003.11.007 Structure 11:1521-1526 (2003)
PubMed id: 14656436  
 
 
Crystal structure of a micro-like calpain reveals a partially activated conformation with low Ca2+ requirement.
G.P.Pal, T.De Veyra, J.S.Elce, Z.Jia.
 
  ABSTRACT  
 
The two Ca2+-dependent cysteine proteases, micro- and m-calpain, are involved in various Ca2+-linked signal pathways but differ markedly in their Ca2+ requirements for activation. We have determined the structure of a micro-like calpain, which has 85% micro-calpain sequence (the first 48 and the last 62 residues of the large subunit are those from m-calpain) and a low Ca2+ requirement. This construct was used because micro-calpain itself is too poorly expressed. The structure of micro-like calpain is very similar in overall fold to that of m-calpain as expected, but differs significantly in two aspects. In comparison with m-calpain, the catalytic triad residues in micro-like calpain, His and Cys, are much closer together in the absence of Ca2+, and significant portions of the Ca2+ binding EF-hand motifs are disordered and more flexible. These structural differences imply that Ca2+-free micro-calpain may represent a partially activated structure, requiring lower Ca2+ concentration to trigger its activation.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. A Section of the Electron Density Map in which the Catalytic Residue His262 Is Shown to Be Well Defined and Stacked with Trp288The map is contoured at 1 s.
 
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 1521-1526) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18793761 D.E.Croall, L.M.Vanhooser, and R.E.Cashon (2008).
Detecting the active conformation of calpain with calpastatin-based reagents.
  Biochim Biophys Acta, 1784, 1676-1686.  
18073773 M.B.Bevers, and R.W.Neumar (2008).
Mechanistic role of calpains in postischemic neurodegeneration.
  J Cereb Blood Flow Metab, 28, 655-673.  
19020622 T.Moldoveanu, K.Gehring, and D.R.Green (2008).
Concerted multi-pronged attack by calpastatin to occlude the catalytic cleft of heterodimeric calpains.
  Nature, 456, 404-408.
PDB code: 3df0
17608959 D.E.Croall, and K.Ersfeld (2007).
The calpains: modular designs and functional diversity.
  Genome Biol, 8, 218.  
17210638 K.Tonami, Y.Kurihara, H.Aburatani, Y.Uchijima, T.Asano, and H.Kurihara (2007).
Calpain 6 is involved in microtubule stabilization and cytoskeletal organization.
  Mol Cell Biol, 27, 2548-2561.  
17942392 R.L.Mellgren, and X.Huang (2007).
Fetuin A stabilizes m-calpain and facilitates plasma membrane repair.
  J Biol Chem, 282, 35868-35877.  
16542156 J.Joy, N.Nalabothula, M.Ghosh, O.Popp, M.Jochum, W.Machleidt, S.Gil-Parrado, and T.A.Holak (2006).
Identification of calpain cleavage sites in the G1 cyclin-dependent kinase inhibitor p19(INK4d).
  Biol Chem, 387, 329-335.  
16623703 M.Averna, R.Stifanese, R.De Tullio, E.Defranchi, F.Salamino, E.Melloni, and S.Pontremoli (2006).
Interaction between catalytically inactive calpain and calpastatin. Evidence for its occurrence in stimulated cells.
  FEBS J, 273, 1660-1668.  
15843151 M.Ghosh, S.Shanker, I.Siwanowicz, K.Mann, W.Machleidt, and T.A.Holak (2005).
Proteolysis of insulin-like growth factor binding proteins (IGFBPs) by calpain.
  Biol Chem, 386, 85-93.  
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 code is shown on the right.