PDBsum entry 1iz2

Go to PDB code: 
protein ligands links
Protein binding PDB id
Protein chain
371 a.a. *
Waters ×101
* Residue conservation analysis
PDB id:
Name: Protein binding
Title: Interactions causing the kinetic trap in serpin protein folding
Structure: Alpha1-antitrypsin. Chain: a. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.20Å     R-factor:   0.211     R-free:   0.278
Authors: H.Im,M.-S.Woo,K.Y.Hwang,M.-H.Yu
Key ref:
H.Im et al. (2002). Interactions causing the kinetic trap in serpin protein folding. J Biol Chem, 277, 46347-46354. PubMed id: 12244055 DOI: 10.1074/jbc.M207682200
19-Sep-02     Release date:   11-Feb-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P01009  (A1AT_HUMAN) -  Alpha-1-antitrypsin
418 a.a.
371 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 10 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   6 terms 
  Biological process     response to inorganic substance   19 terms 
  Biochemical function     protein binding     6 terms  


DOI no: 10.1074/jbc.M207682200 J Biol Chem 277:46347-46354 (2002)
PubMed id: 12244055  
Interactions causing the kinetic trap in serpin protein folding.
H.Im, M.S.Woo, K.Y.Hwang, M.H.Yu.
Conformational transition is fundamental to the mechanism of functional regulation in proteins, and serpins (serine protease inhibitors) can provide insight into this process. Serpins are metastable in their native forms, and they ordinarily undergo conformational transition to a stable state only when they form a tight complex with target proteases. The metastable native form is thus considered to be a kinetically trapped folding intermediate. We sought to understand the nature of the serpin kinetic trap as a step toward discovering how conformational transition is regulated. We found that mutations of the B/C beta-barrel of native alpha(1)-antitrypsin, a prototypical serpin, allowed conversion of the molecule into a more stable state. A 2.2 A resolution crystal structure of the stable form (PDB code, ) showed that the reactive site loop is inserted into an A beta-sheet, as in the latent plasminogen activator inhibitor-1. Mutational analyses suggest strongly that interactions not found in the final stable form cause the kinetic trap in serpin protein folding.
  Selected figure(s)  
Figure 1.
Fig. 1. Conversion of [1]AT into a stable conformation. Soluble monomeric forms of wild-type, V364A, a double mutant of I229A/V364A, and K335D were incubated in 10 mM phosphate, 50 mM NaCl, 1 mM EDTA, 1 mM -mercaptoethanol, pH 6.5, at 30 °C for 24 h, and appearance of a urea-stable conformation was examined by transverse urea gradient gel electrophoresis (30). The transverse urea gradient gels contained a gradient of 0~8 M urea perpendicular to the direction of electrophoresis. Open arrows indicate the migration position of the native form of [1]AT, and filled arrows indicate that of the stable form of [1]AT.
Figure 3.
Fig. 3. Structural examination of the stable conformation of [1]AT. A, overall structure of the stable conformation of V364A/M7 [1]AT. The reactive site loop and strand 1 of C sheet (s1C) are shown in blue. The electron density map of the region from Met-358 to Ala-364 (the mutation site) is shown in the inset. An additive, N-octanoyl sucrose, which was partially inserted into the C -sheet, is shown in red. B, overlap of C atoms of the stable structure of [1]AT (thick line) and the latent PAI-1 ( thin line). Strands s4A of two structures were aligned. The reactive site loop and s1C of the stable [1]AT molecule are shown in blue, and those of the latent PAI-1 are shown in purple. The residue position of Ala-364 of [1]AT is highlighted by an orange dot. C, the sites of various destabilizing mutations on the native [1]AT structure (PDB code, 1HP7; Ref. 53). The reactive site loop and s1C are shown in blue. Strands s2C, s1B, and s3B are shown in green, in which destabilizing mutations that promote the conversion to the stable form are mapped. Side chains of the effective mutations are colored green and pink. The residue sites of the destabilizing mutations that did not promote the conversion are indicated by cyan beads, which are V55P (helix B), I76A (helix C), L112A (s2A), N186A (s3A), F208A (s4C), L240A (s2B), F252A (s3B), V311A (helix I1), H334A (s5A), K335D (s5A), F370A (s4B), and I375A (s4B). Inset, a close-up view of the B/C -barrel region.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 46347-46354) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19843463 A.Chiou, P.Hägglöf, A.Orte, A.Y.Chen, P.D.Dunne, D.Belorgey, S.Karlsson-Li, D.A.Lomas, and D.Klenerman (2009).
Probing neuroserpin polymerization and interaction with amyloid-beta peptides using single molecule fluorescence.
  Biophys J, 97, 2306-2315.  
19245336 B.Gooptu, and D.A.Lomas (2009).
Conformational pathology of the serpins: themes, variations, and therapeutic strategies.
  Annu Rev Biochem, 78, 147-176.  
19232354 B.Gooptu, E.Miranda, I.Nobeli, M.Mallya, A.Purkiss, S.C.Brown, C.Summers, R.L.Phillips, D.A.Lomas, and T.E.Barrett (2009).
Crystallographic and cellular characterisation of two mechanisms stabilising the native fold of alpha1-antitrypsin: implications for disease and drug design.
  J Mol Biol, 387, 857-868.
PDB codes: 3drm 3dru
19136720 J.H.Baek, W.S.Yang, C.Lee, and M.H.Yu (2009).
Functional unfolding of alpha1-antitrypsin probed by hydrogen-deuterium exchange coupled with mass spectrometry.
  Mol Cell Proteomics, 8, 1072-1081.  
18564103 K.Yamashita, S.Nakashima, F.You, S.Hayashi, and T.Iwama (2009).
Overexpression of immediate early gene X-1 (IEX-1) enhances gamma-radiation-induced apoptosis of human glioma cell line, U87-MG.
  Neuropathology, 29, 20-24.  
18515400 G.Lois, J.Blawzdziewicz, and C.S.O'Hern (2008).
Reliable protein folding on complex energy landscapes: the free energy reaction path.
  Biophys J, 95, 2692-2701.  
17203395 M.J.Kim, Y.K.Lee, H.K.Lee, and H.Im (2007).
Characterization of cold-shock protein A of Antarctic Streptomyces sp. AA8321.
  Protein J, 26, 51-59.  
17600149 Y.R.Na, and H.Im (2007).
Specific interactions of serpins in their native forms attenuate their conformational transitions.
  Protein Sci, 16, 1659-1666.  
16773239 E.Karnaukhova, Y.Ophir, and B.Golding (2006).
Recombinant human alpha-1 proteinase inhibitor: towards therapeutic use.
  Amino Acids, 30, 317-332.  
16820297 J.A.Huntington (2006).
Shape-shifting serpins--advantages of a mobile mechanism.
  Trends Biochem Sci, 31, 427-435.  
15576554 Y.R.Na, and H.Im (2005).
The length of the reactive center loop modulates the latency transition of plasminogen activator inhibitor-1.
  Protein Sci, 14, 55-63.  
15170041 D.A.Lomas, and H.Parfrey (2004).
Alpha1-antitrypsin deficiency. 4: Molecular pathophysiology.
  Thorax, 59, 529-535.  
15291813 D.Belorgey, L.K.Sharp, D.C.Crowther, M.Onda, J.Johansson, and D.A.Lomas (2004).
Neuroserpin Portland (Ser52Arg) is trapped as an inactive intermediate that rapidly forms polymers: implications for the epilepsy seen in the dementia FENIB.
  Eur J Biochem, 271, 3360-3367.  
14567688 G.E.Blouse, M.J.Perron, J.O.Kvassman, S.Yunus, J.H.Thompson, R.L.Betts, L.C.Lutter, and J.D.Shore (2003).
Mutation of the highly conserved tryptophan in the serpin breach region alters the inhibitory mechanism of plasminogen activator inhibitor-1.
  Biochemistry, 42, 12260-12272.  
12581670 M.Laskowski, M.A.Qasim, and Z.Yi (2003).
Additivity-based prediction of equilibrium constants for some protein-protein associations.
  Curr Opin Struct Biol, 13, 130-139.  
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 codes are shown on the right.