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PDBsum entry 1oo8

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Hydrolase inhibitor PDB id
1oo8
Jmol
Contents
Protein chain
370 a.a. *
Waters ×123
* Residue conservation analysis
PDB id:
1oo8
Name: Hydrolase inhibitor
Title: Crystal structure of a1pi-pittsburgh in the native conformation
Structure: Alpha-1-antitrypsin precursor. Chain: a. Fragment: residues 26-418. Synonym: alpha-1 protease inhibitor, alpha-1- antiproteinase, pro0684/pro2209. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: liver. Tissue: hepatocytes. Cell: neutrophils. Cellular_location: cytoplasm. Gene: serpina1 or pi or aat. Expressed in: escherichia coli.
Resolution:
2.65Å     R-factor:   0.188     R-free:   0.193
Authors: A.Dementiev,M.Simonovic,K.Volz,P.G.Gettins
Key ref:
A.Dementiev et al. (2003). Canonical inhibitor-like interactions explain reactivity of alpha1-proteinase inhibitor Pittsburgh and antithrombin with proteinases. J Biol Chem, 278, 37881-37887. PubMed id: 12860985 DOI: 10.1074/jbc.M305195200
Date:
03-Mar-03     Release date:   05-Aug-03    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01009  (A1AT_HUMAN) -  Alpha-1-antitrypsin
Seq:
Struc:
418 a.a.
370 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   7 terms 
  Biological process     response to inorganic substance   19 terms 
  Biochemical function     protein binding     7 terms  

 

 
DOI no: 10.1074/jbc.M305195200 J Biol Chem 278:37881-37887 (2003)
PubMed id: 12860985  
 
 
Canonical inhibitor-like interactions explain reactivity of alpha1-proteinase inhibitor Pittsburgh and antithrombin with proteinases.
A.Dementiev, M.Simonovic, K.Volz, P.G.Gettins.
 
  ABSTRACT  
 
The serpin antithrombin is a slow thrombin inhibitor that requires heparin to enhance its reaction rate. In contrast, alpha1-proteinase inhibitor (alpha1PI) Pittsburgh (P1 Met --> Arg natural variant) inhibits thrombin 17 times faster than pentasaccharide heparin-activated antithrombin. We present here x-ray structures of free and S195A trypsin-bound alpha1PI Pittsburgh, which show that the reactive center loop (RCL) possesses a canonical conformation in the free serpin that does not change upon binding to S195A trypsin and that contacts the proteinase only between P2 and P2'. By inference from the structure of heparin cofactor II bound to S195A thrombin, this RCL conformation is also appropriate for binding to thrombin. Reaction rates of trypsin and thrombin with alpha1PI Pittsburgh and antithrombin and their P2 variants show that the low antithrombin-thrombin reaction rate results from the antithrombin RCL sequence at P2 and implies that, in solution, the antithrombin RCL must be in a similar canonical conformation to that found here for alpha1PI Pittsburgh, even in the nonheparin-activated state. This suggests a general, limited, canonical-like interaction between serpins and proteinases in their Michaelis complexes.
 
  Selected figure(s)  
 
Figure 4.
FIG. 4. Thrombin and its interactions with inhibitors. a, superposition, in stereo, of thrombin or S195A thrombin structures of complexes with PPACK (gold) (Protein Data Bank code 1HAI [PDB] ), with BPTI (green) (Protein Data Bank code 1BTH [PDB] ), and with heparin cofactor II (red) (Protein Data Bank code 1JMO [PDB] ), showing the identical conformations of all regions except the surface loops flanking the active site, particularly the 60 loop and 150 loop. b, stereo representation of the P5-P5' residues of [1]PI Pittsburgh (cyan) from the noncovalent complex with S195A trypsin docked into the thrombin structure found in the noncovalent complex of S195A thrombin with heparin cofactor II (HCII in magenta).
Figure 5.
FIG. 5. Antithrombin RCL conformation and modeled interaction with thrombin. a, superposition, in stereo, of the conformations of P5-P5' residues of [1]PI Pittsburgh from its noncovalent complex with S195A trypsin and of pentasacharide-activated antithrombin from a structure of the heterodimer (orange) (Protein Data Bank code 1AZX [PDB] ). These RCLs are aligned such that the P1 residues have the same horizontal position. The view is rotated 90° anticlockwise relative to Fig. 1b. b, stereo representation of the P5-P5' residues of antithrombin from the x-ray structure of antithrombin heterodimer docked into the thrombin structure found in the noncovalent complex of S195A thrombin with heparin cofactor II, showing inappropriate positioning relative to the catalytic triad and unfavorable interactions with surface loops.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 37881-37887) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21080914 L.Meinert Niclasen, J.G.Olsen, R.Dagil, Z.Qing, O.E.Sørensen, and B.B.Kragelund (2011).
Streptococcal pyogenic exotoxin B (SpeB) boosts the contact system via binding of α-1 antitrypsin.
  Biochem J, 434, 123-132.  
20615447 P.Goettig, V.Magdolen, and H.Brandstetter (2010).
Natural and synthetic inhibitors of kallikrein-related peptidases (KLKs).
  Biochimie, 92, 1546-1567.  
19629171 C.Drögemüller, D.Becker, A.Brunner, B.Haase, P.Kircher, F.Seeliger, M.Fehr, U.Baumann, K.Lindblad-Toh, and T.Leeb (2009).
A missense mutation in the SERPINH1 gene in Dachshunds with osteogenesis imperfecta.
  PLoS Genet, 5, e1000579.  
19010776 G.Izaguirre, A.R.Rezaie, and S.T.Olson (2009).
Engineering functional antithrombin exosites in alpha1-proteinase inhibitor that specifically promote the inhibition of factor Xa and factor IXa.
  J Biol Chem, 284, 1550-1558.  
19162547 M.Cugno, A.Zanichelli, F.Foieni, S.Caccia, and M.Cicardi (2009).
C1-inhibitor deficiency and angioedema: molecular mechanisms and clinical progress.
  Trends Mol Med, 15, 69-78.  
18063751 R.H.Law, T.Sofian, W.T.Kan, A.J.Horvath, C.R.Hitchen, C.G.Langendorf, A.M.Buckle, J.C.Whisstock, and P.B.Coughlin (2008).
X-ray crystal structure of the fibrinolysis inhibitor alpha2-antiplasmin.
  Blood, 111, 2049-2052.
PDB code: 2r9y
18060440 T.H.Roberts, and J.Hejgaard (2008).
Serpins in plants and green algae.
  Funct Integr Genomics, 8, 1.  
  19164889 D.Belorgey, P.Hägglöf, S.Karlsson-Li, and D.A.Lomas (2007).
Protein misfolding and the serpinopathies.
  Prion, 1, 15-20.  
17962402 L.Liu, N.Mushero, L.Hedstrom, and A.Gershenson (2007).
Short-lived protease serpin complexes: partial disruption of the rat trypsin active site.
  Protein Sci, 16, 2403-2411.  
16619025 D.J.Johnson, W.Li, T.E.Adams, and J.A.Huntington (2006).
Antithrombin-S195A factor Xa-heparin structure reveals the allosteric mechanism of antithrombin activation.
  EMBO J, 25, 2029-2037.
PDB code: 2gd4
16820297 J.A.Huntington (2006).
Shape-shifting serpins--advantages of a mobile mechanism.
  Trends Biochem Sci, 31, 427-435.  
17079131 J.C.Whisstock, and S.P.Bottomley (2006).
Molecular gymnastics: serpin structure, folding and misfolding.
  Curr Opin Struct Biol, 16, 761-768.  
16737556 R.H.Law, Q.Zhang, S.McGowan, A.M.Buckle, G.A.Silverman, W.Wong, C.J.Rosado, C.G.Langendorf, R.N.Pike, P.I.Bird, and J.C.Whisstock (2006).
An overview of the serpin superfamily.
  Genome Biol, 7, 216.  
17042782 S.Skeldal, J.V.Larsen, K.E.Pedersen, H.H.Petersen, R.Egelund, A.Christensen, J.K.Jensen, J.Gliemann, and P.A.Andreasen (2006).
Binding areas of urokinase-type plasminogen activator-plasminogen activator inhibitor-1 complex for endocytosis receptors of the low-density lipoprotein receptor family, determined by site-directed mutagenesis.
  FEBS J, 273, 5143-5159.  
15632287 L.D.Tesch, M.P.Raghavendra, T.Bedsted-Faarvang, P.G.Gettins, and S.T.Olson (2005).
Specificity and reactive loop length requirements for crmA inhibition of serine proteases.
  Protein Sci, 14, 533-542.  
15311268 A.Dementiev, M.Petitou, J.M.Herbert, and P.G.Gettins (2004).
The ternary complex of antithrombin-anhydrothrombin-heparin reveals the basis of inhibitor specificity.
  Nat Struct Mol Biol, 11, 863-867.
PDB code: 1sr5
15311269 W.Li, D.J.Johnson, C.T.Esmon, and J.A.Huntington (2004).
Structure of the antithrombin-thrombin-heparin ternary complex reveals the antithrombotic mechanism of heparin.
  Nat Struct Mol Biol, 11, 857-862.
PDB code: 1tb6
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.