PDBsum entry 2h4y

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Hydrolase/hydrolase inhibitor PDB id
Jmol PyMol
Protein chains
163 a.a. *
87 a.a. *
Waters ×189
* Residue conservation analysis
PDB id:
Name: Hydrolase/hydrolase inhibitor
Title: Crystal structure of human caspase-1 (arg286->lys) in comple [2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propion 4-oxo-pentanoic acid (z-vad-fmk)
Structure: Caspase-1. Chain: a. Fragment: p20 subunit, residues 120-297. Engineered: yes. Mutation: yes. Caspase-1. Chain: b. Fragment: p10 subunit, residues 317-404. Engineered: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: casp1, il1bc, il1bce. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes
1.90Å     R-factor:   0.205     R-free:   0.235
Authors: J.M.Scheer,J.A.Wells,M.J.Romanowski
Key ref:
D.Datta et al. (2008). An allosteric circuit in caspase-1. J Mol Biol, 381, 1157-1167. PubMed id: 18590738 DOI: 10.1016/j.jmb.2008.06.040
25-May-06     Release date:   11-Mar-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P29466  (CASP1_HUMAN) -  Caspase-1
404 a.a.
163 a.a.*
Protein chain
Pfam   ArchSchema ?
P29466  (CASP1_HUMAN) -  Caspase-1
404 a.a.
87 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.  - Caspase-1.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Release of interleukin 1-beta by specific cleavage at 116-Asp-|-Ala-117 and 27-Asp-|-Gly-28 bonds in precursor. Also hydrolyzes the small- molecule substrate, Ac-Tyr-Val-Ala-Asp-|-NHMec.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     cysteine-type peptidase activity     1 term  


DOI no: 10.1016/j.jmb.2008.06.040 J Mol Biol 381:1157-1167 (2008)
PubMed id: 18590738  
An allosteric circuit in caspase-1.
D.Datta, J.M.Scheer, M.J.Romanowski, J.A.Wells.
Structural studies of caspase-1 reveal that the dimeric thiol protease can exist in two states: in an on-state, when the active site is occupied, or in an off-state, when the active site is empty or when the enzyme is bound by a synthetic allosteric ligand at the dimer interface approximately 15 A from the active site. A network of 21 hydrogen bonds from nine side chains connecting the active and allosteric sites change partners when going between the on-state and the off-state. Alanine-scanning mutagenesis of these nine side chains shows that only two of them-Arg286 and Glu390, which form a salt bridge-have major effects, causing 100- to 200-fold reductions in catalytic efficiency (k(cat)/K(m)). Two neighbors, Ser332 and Ser339, have minor effects, causing 4- to 7-fold reductions. A more detailed mutational analysis reveals that the enzyme is especially sensitive to substitutions of the salt bridge: even a homologous R286K substitution causes a 150-fold reduction in k(cat)/K(m). X-ray crystal structures of these variants suggest the importance of both the salt bridge interaction and the coordination of solvent water molecules near the allosteric binding pocket. Thus, only a small subset of side chains from the larger hydrogen bonding network is critical for activity. These form a contiguous set of interactions that run from one active site through the allosteric site at the dimer interface and onto the second active site. This subset constitutes a functional allosteric circuit or "hot wire" that promotes site-to-site coupling.
  Selected figure(s)  
Figure 2.
Fig. 2. Residues that form an H-bonding network and a salt bridge connecting the active and allosteric ligand sites of caspase-1. In the on-state conformation (left), many H-bond interactions involving polar side chains that are not preserved in the off-state conformation (right) are formed. Dashed lines indicate a distance of < 3.5 Å between two polar atoms. Yellow spheres represent the z-VAD-FMK active-site inhibitor in the on-state structure (PDB ID code 2HBQ);^4 green spheres represent the allosteric inhibitor in the off-state structure (PDB ID code 2FQQ).^4 The active-site cysteine (Cys285) is replaced with alanine (orange) in the off-state structure, and Thr388 is hidden behind the allosteric inhibitor.
Figure 3.
Fig. 3. The left panel shows a size- and color-coded representation of residues important for wild-type caspase-1 activity. Larger residues had a larger impact when replaced with alanine; red, green, and blue indicate a > 100-fold, > 2-fold, and < 2-fold decrease in k[cat]/K[m] relative to wild-type. The allosteric site is located to the right of Glu390. The right panel shows an expanded view of the caspase-1 dimer. A circuit of residues connects the two active sites to the central allosteric site via the Arg286-Glu390 salt bridges. The yellow spheres represent the z-VAD-FMK active-site inhibitor.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 381, 1157-1167) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21317893 A.Shen, P.J.Lupardus, M.M.Gersch, A.W.Puri, V.E.Albrow, K.C.Garcia, and M.Bogyo (2011).
Defining an allosteric circuit in the cysteine protease domain of Clostridium difficile toxins.
  Nat Struct Mol Biol, 18, 364-371.
PDB code: 3pee
20539873 A.Shen (2010).
Allosteric regulation of protease activity by small molecules.
  Mol Biosyst, 6, 1431-1443.  
20140189 F.P.Davis, and A.Sali (2010).
The overlap of small molecule and protein binding sites within families of protein structures.
  PLoS Comput Biol, 6, e1000668.  
20819242 P.I.Zhuravlev, and G.A.Papoian (2010).
Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework.
  Q Rev Biophys, 43, 295-332.  
19679084 A.del Sol, C.J.Tsai, B.Ma, and R.Nussinov (2009).
The origin of allosteric functional modulation: multiple pre-existing pathways.
  Structure, 17, 1042-1050.  
19473994 C.Pop, and G.S.Salvesen (2009).
Human caspases: activation, specificity, and regulation.
  J Biol Chem, 284, 21777-21781.  
19581639 J.A.Hardy, and J.A.Wells (2009).
Dissecting an allosteric switch in caspase-7 using chemical and mutational probes.
  J Biol Chem, 284, 26063-26069.  
19208804 J.Gao, S.S.Sidhu, and J.A.Wells (2009).
Two-state selection of conformation-specific antibodies.
  Proc Natl Acad Sci U S A, 106, 3071-3076.  
19788411 J.Walters, C.Pop, F.L.Scott, M.Drag, P.Swartz, C.Mattos, G.S.Salvesen, and A.C.Clark (2009).
A constitutively active and uninhibitable caspase-3 zymogen efficiently induces apoptosis.
  Biochem J, 424, 335-345.
PDB code: 3itn
19703402 N.Halabi, O.Rivoire, S.Leibler, and R.Ranganathan (2009).
Protein sectors: evolutionary units of three-dimensional structure.
  Cell, 138, 774-786.  
19816556 O.N.Demerdash, M.D.Daily, and J.C.Mitchell (2009).
Structure-based predictive models for allosteric hot spots.
  PLoS Comput Biol, 5, e1000531.  
19694615 R.Baumgartner, G.Meder, C.Briand, A.Decock, A.D'arcy, U.Hassiepen, R.Morse, and M.Renatus (2009).
The crystal structure of caspase-6, a selective effector of axonal degeneration.
  Biochem J, 423, 429-439.
PDB code: 2wdp
19530232 W.A.Witkowski, and J.A.Hardy (2009).
L2' loop is critical for caspase-7 active site formation.
  Protein Sci, 18, 1459-1468.
PDB code: 3h1p
19021141 P.Hauske, C.Ottmann, M.Meltzer, M.Ehrmann, and M.Kaiser (2008).
Allosteric regulation of proteases.
  Chembiochem, 9, 2920-2928.  
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.