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PDBsum entry 1mtp

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protein Protein-protein interface(s) links
Structural genomics PDB id
1mtp
Jmol
Contents
Protein chains
320 a.a. *
35 a.a. *
Waters ×604
* Residue conservation analysis
PDB id:
1mtp
Name: Structural genomics
Title: The x-ray crystal structure of a serpin from a thermophilic prokaryote
Structure: Serine proteinase inhibitor (serpin), chain a. Chain: a. Fragment: chain a, residue 55-377. Engineered: yes. Serine proteinase inhibitor (serpin), chain b. Chain: b. Fragment: chain b, residue 378-420. Engineered: yes
Source: Thermobifida fusca. Organism_taxid: 2021. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
1.50Å     R-factor:   0.195     R-free:   0.223
Authors: J.A.Irving,L.D.Cabrita,J.Rossjohn,R.N.Pike,S.P.Bottomley, J.C.Whisstock
Key ref:
J.A.Irving et al. (2003). The 1.5 A crystal structure of a prokaryote serpin: controlling conformational change in a heated environment. Structure, 11, 387-397. PubMed id: 12679017 DOI: 10.1016/S0969-2126(03)00057-1
Date:
21-Sep-02     Release date:   15-Apr-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q47NK3  (Q47NK3_THEFY) -  Proteinase inhibitor I4, serpin
Seq:
Struc:
366 a.a.
320 a.a.*
Protein chain
Pfam   ArchSchema ?
Q47NK3  (Q47NK3_THEFY) -  Proteinase inhibitor I4, serpin
Seq:
Struc:
366 a.a.
35 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular space   1 term 

 

 
DOI no: 10.1016/S0969-2126(03)00057-1 Structure 11:387-397 (2003)
PubMed id: 12679017  
 
 
The 1.5 A crystal structure of a prokaryote serpin: controlling conformational change in a heated environment.
J.A.Irving, L.D.Cabrita, J.Rossjohn, R.N.Pike, S.P.Bottomley, J.C.Whisstock.
 
  ABSTRACT  
 
Serpins utilize conformational change to inhibit target proteinases; the price paid for this conformational flexibility is that many undergo temperature-induced polymerization. Despite this thermolability, serpins are present in the genomes of thermophilic prokaryotes, and here we characterize the first such serpin, thermopin. Thermopin is a proteinase inhibitor and, in comparison with human alpha(1)-antitrypsin, possesses enhanced stability at 60 degrees C. The 1.5 A crystal structure reveals novel structural features in regions implicated in serpin folding and stability. Thermopin possesses a C-terminal "tail" that interacts with the top of the A beta sheet and plays an important role in the folding/unfolding of the molecule. These data provide evidence as to how this unusual serpin has adapted to fold and function in a heated environment.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. A Schematic Summarizing the Inhibitory Mechanism of SerpinsThe RCL is the region responsible for interacting with target proteinases and is at the top of the molecule. Residues within the RCL are numbered according to Schecter and Berger [78], in which the residues of a peptide substrate are designated P[n]...P[2], P[1], and P[1]'...P[n]', and interact with corresponding subsites in the proteinase, designated S[n]...S[2], S[1], and S[1]'...S[n]'; cleavage occurs by definition between the P[1] and P[1]' positions. The proteinase (denoted by "P") recognizes the RCL sequence and cleaves the serpin between P[1] and P[1]'; after this, prior to hydrolysis of the acyl bond that links enzyme to inhibitor, the RCL inserts into the central "A" b sheet. The proteinase is thereby translocated to the distal end of the molecule, where it is compressed against the base of the serpin and its active site is distorted.
 
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 387-397) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19394412 C.Suwanchaichinda, and M.R.Kanost (2009).
The serpin gene family in Anopheles gambiae.
  Gene, 442, 47-54.  
19624115 T.Sengupta, Y.Tsutsui, and P.L.Wintrode (2009).
Local and global effects of a cavity filling mutation in a metastable serpin.
  Biochemistry, 48, 8233-8240.  
18060440 T.H.Roberts, and J.Hejgaard (2008).
Serpins in plants and green algae.
  Funct Integr Genomics, 8, 1.  
17635906 L.D.Cabrita, J.A.Irving, M.C.Pearce, J.C.Whisstock, and S.P.Bottomley (2007).
Aeropin from the extremophile Pyrobaculum aerophilum bypasses the serpin misfolding trap.
  J Biol Chem, 282, 26802-26809.  
17442346 P.Chowdhury, W.Wang, S.Lavender, M.R.Bunagan, J.W.Klemke, J.Tang, J.G.Saven, B.S.Cooperman, and F.Gai (2007).
Fluorescence correlation spectroscopic study of serpin depolymerization by computationally designed peptides.
  J Mol Biol, 369, 462-473.  
17557112 Q.Zhang, A.M.Buckle, R.H.Law, M.C.Pearce, L.D.Cabrita, G.J.Lloyd, J.A.Irving, A.I.Smith, K.Ruzyla, J.Rossjohn, S.P.Bottomley, and J.C.Whisstock (2007).
The N terminus of the serpin, tengpin, functions to trap the metastable native state.
  EMBO Rep, 8, 658-663.
PDB codes: 2pee 2pef
16627467 D.Ivanov, C.Emonet, F.Foata, M.Affolter, M.Delley, M.Fisseha, S.Blum-Sperisen, S.Kochhar, and F.Arigoni (2006).
A serpin from the gut bacterium Bifidobacterium longum inhibits eukaryotic elastase-like serine proteases.
  J Biol Chem, 281, 17246-17252.  
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.  
16796673 S.Kang, Y.Barak, R.Lamed, E.A.Bayer, and M.Morrison (2006).
The functional repertoire of prokaryote cellulosomes includes the serpin superfamily of serine proteinase inhibitors.
  Mol Microbiol, 60, 1344-1354.  
16796670 W.H.Schwarz, and V.V.Zverlov (2006).
Protease inhibitors in bacteria: an emerging concept for the regulation of bacterial protein complexes?
  Mol Microbiol, 60, 1323-1326.  
16176261 J.C.Whisstock, S.P.Bottomley, P.I.Bird, R.N.Pike, and P.Coughlin (2005).
Serpins 2005 - fun between the beta-sheets. Meeting report based upon presentations made at the 4th International Symposium on Serpin Structure, Function and Biology (Cairns, Australia).
  FEBS J, 272, 4868-4873.  
15590653 K.F.Fulton, A.M.Buckle, L.D.Cabrita, J.A.Irving, R.E.Butcher, I.Smith, S.Reeve, A.M.Lesk, S.P.Bottomley, J.Rossjohn, and J.C.Whisstock (2005).
The high resolution crystal structure of a native thermostable serpin reveals the complex mechanism underpinning the stressed to relaxed transition.
  J Biol Chem, 280, 8435-8442.
PDB code: 1sng
15638455 T.H.Roberts, J.Hejgaard, N.F.Saunders, R.Cavicchioli, and P.M.Curmi (2004).
Serpins in unicellular Eukarya, Archaea, and Bacteria: sequence analysis and evolution.
  J Mol Evol, 59, 437-447.  
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.