spacer
spacer

PDBsum entry 2ant

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Serpin PDB id
2ant
Jmol
Contents
Protein chains
398 a.a. *
419 a.a. *
Ligands
NAA ×2
Waters ×79
* Residue conservation analysis
PDB id:
2ant
Name: Serpin
Title: The 2.6 a structure of antithrombin indicates a conformational change at the heparin binding site
Structure: Antithrombin. Chain: l, i. Other_details: antithrombin crystallised as a dimer between latent molecule and one active molecule
Source: Homo sapiens. Human. Organism_taxid: 9606. Tissue: plasma
Biol. unit: Monomer (from PDB file)
Resolution:
2.60Å     R-factor:   0.217     R-free:   0.290
Authors: R.Skinner,J.-P.Abrahams,J.C.Whisstock,A.M.Lesk,R.W.Carrell, M.R.Wardell
Key ref:
R.Skinner et al. (1997). The 2.6 A structure of antithrombin indicates a conformational change at the heparin binding site. J Mol Biol, 266, 601-609. PubMed id: 9067613 DOI: 10.1006/jmbi.1996.0798
Date:
28-Jan-97     Release date:   16-Jun-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01008  (ANT3_HUMAN) -  Antithrombin-III
Seq:
Struc:
464 a.a.
398 a.a.
Protein chain
Pfam   ArchSchema ?
P01008  (ANT3_HUMAN) -  Antithrombin-III
Seq:
Struc:
464 a.a.
419 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   5 terms 
  Biological process     regulation of blood coagulation, intrinsic pathway   8 terms 
  Biochemical function     protein binding     5 terms  

 

 
DOI no: 10.1006/jmbi.1996.0798 J Mol Biol 266:601-609 (1997)
PubMed id: 9067613  
 
 
The 2.6 A structure of antithrombin indicates a conformational change at the heparin binding site.
R.Skinner, J.P.Abrahams, J.C.Whisstock, A.M.Lesk, R.W.Carrell, M.R.Wardell.
 
  ABSTRACT  
 
The crystal structure of a dimeric form of intact antithrombin has been solved to 2.6 A, representing the highest-resolution structure of an active, inhibitory serpin to date. The crystals were grown under microgravity conditions on Space Shuttle mission STS-67. The overall confidence in the structure, determined earlier from lower resolution data, is increased and new insights into the structure-function relationship are gained. Clear and continuous electron density is present for the reactive centre loop region P12 to P14 inserting into the top of the A-beta-sheet. Areas of the extended amino terminus, unique to antithrombin and important in the binding of the glycosaminoglycan heparin, can now be traced further than in the earlier structures. As in the earlier studies, the crystals contain one active and one latent molecule per asymmetric unit. Better definition of the electron density surrounding the D-helix and of the residues implicated in the binding of the heparin pentasaccharide (Arg47, Lys114, Lys125, Arg129) provides an insight into the change of affinity of binding that accompanies the change in conformation. In particular, the observed hydrogen bonding of these residues to the body of the molecule in the latent form explains the mechanism for the release of newly formed antithrombin-protease complexes into the circulation for catabolic removal.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. A representation of the heparin pentasaccharide binding site showing the D-helix (red), the A-helix (green) and the side-chains of the pentasaccharide binding residues (blue). (a) In the active conformation the D-helix is kinked and all of the pentasaccharide binding residues are oriented towards the binding site. (b) In the latent conformation, the D-helix is straight and all of the pentasaccharide binding residues are either hydrogen-bonding to other residues or pointing away from the binding site or both. The ribbon diagram was produced by MOLSCRIPT [Kraulis 1991].
Figure 2.
Figure 2. 2 F[o]−F[c] map (contoured at 1.0σ) of Lys125 and the surrounding region. (a) In the latent molecule the electron density for the side-chain of Lys125 is well defined and the hydrogen bond between this side-chain and the carboxyl oxygen atom of Ile7 can be clearly seen. (b) In the active molecule the electron density is less well defined for the end portion of the side-chain and no hydrogen bonding can be observed.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 266, 601-609) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19893573 D.Kaiserman, and P.I.Bird (2010).
Control of granzymes by serpins.
  Cell Death Differ, 17, 586-595.  
19320820 J.S.Bae, and A.R.Rezaie (2009).
Mutagenesis studies toward understanding the intracellular signaling mechanism of antithrombin.
  J Thromb Haemost, 7, 803-810.  
19172319 V.Chandrasekaran, C.J.Lee, P.Lin, R.E.Duke, and L.G.Pedersen (2009).
A computational modeling and molecular dynamics study of the Michaelis complex of human protein Z-dependent protease inhibitor (ZPI) and factor Xa (FXa).
  J Mol Model, 15, 897-911.  
  19712578 Y.Chen, W.Tan, S.Qin, J.Zhang, H.Bu, Y.Li, Y.Lu, and J.Cheng (2009).
Cloning of the full-length cDNA of porcine antithrombin III and comparison with its human homolog.
  Comp Med, 59, 372-377.  
19543696 Z.Volovyk, D.M.Monroe, Y.Qi, R.Becker, and M.Hoffman (2009).
A rationally designed heparin, M118, has anticoagulant activity similar to unfractionated heparin and different from Lovenox in a cell-based model of thrombin generation.
  J Thromb Thrombolysis, 28, 132-139.  
18375953 B.Richard, R.Swanson, S.Schedin-Weiss, B.Ramirez, G.Izaguirre, P.G.Gettins, and S.T.Olson (2008).
Characterization of the conformational alterations, reduced anticoagulant activity, and enhanced antiangiogenic activity of prelatent antithrombin.
  J Biol Chem, 283, 14417-14429.  
18436534 S.H.Li, N.V.Gorlatova, D.A.Lawrence, and B.S.Schwartz (2008).
Structural differences between active forms of plasminogen activator inhibitor type 1 revealed by conformationally sensitive ligands.
  J Biol Chem, 283, 18147-18157.  
17875649 G.Izaguirre, R.Swanson, S.M.Raja, A.R.Rezaie, and S.T.Olson (2007).
Mechanism by which exosites promote the inhibition of blood coagulation proteases by heparin-activated antithrombin.
  J Biol Chem, 282, 33609-33622.  
17488724 L.Beinrohr, V.Harmat, J.Dobó, Z.Lörincz, P.Gál, and P.Závodszky (2007).
C1 inhibitor serpin domain structure reveals the likely mechanism of heparin potentiation and conformational disease.
  J Biol Chem, 282, 21100-21109.
PDB code: 2oay
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.  
17040907 W.Zhang, R.Swanson, Y.Xiong, B.Richard, and S.T.Olson (2006).
Antiangiogenic antithrombin blocks the heparan sulfate-dependent binding of proangiogenic growth factors to their endothelial cell receptors: evidence for differential binding of antiangiogenic and anticoagulant forms of antithrombin to proangiogenic heparan sulfate domains.
  J Biol Chem, 281, 37302-37310.  
15930636 R.A.Judge, E.H.Snell, M.J.van der Woerd, and E.H.Snell (2005).
Extracting trends from two decades of microgravity macromolecular crystallization history.
  Acta Crystallogr D Biol Crystallogr, 61, 763-771.  
16176258 R.N.Pike, A.M.Buckle, B.F.le Bonniec, and F.C.Church (2005).
Control of the coagulation system by serpins. Getting by with a little help from glycosaminoglycans.
  FEBS J, 272, 4842-4851.  
16131762 R.Willaert, I.Zegers, L.Wyns, and M.Sleutel (2005).
Protein crystallization in hydrogel beads.
  Acta Crystallogr D Biol Crystallogr, 61, 1280-1288.  
15905187 W.Zhang, R.Swanson, G.Izaguirre, Y.Xiong, L.F.Lau, and S.T.Olson (2005).
The heparin-binding site of antithrombin is crucial for antiangiogenic activity.
  Blood, 106, 1621-1628.  
15743473 X.Chang, R.Yamada, and K.Yamamoto (2005).
Inhibition of antithrombin by hyaluronic acid may be involved in the pathogenesis of rheumatoid arthritis.
  Arthritis Res Ther, 7, R268-R273.  
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
15613023 A.Mushunje, G.Evans, S.O.Brennan, R.W.Carrell, and A.Zhou (2004).
Latent antithrombin and its detection, formation and turnover in the circulation.
  J Thromb Haemost, 2, 2170-2177.  
14705167 U.R.Desai (2004).
New antithrombin-based anticoagulants.
  Med Res Rev, 24, 151-181.  
12414799 A.S.Robertson, D.Belorgey, K.S.Lilley, D.A.Lomas, D.Gubb, and T.R.Dafforn (2003).
Characterization of the necrotic protein that regulates the Toll-mediated immune response in Drosophila.
  J Biol Chem, 278, 6175-6180.  
14532267 G.Izaguirre, W.Zhang, R.Swanson, T.Bedsted, and S.T.Olson (2003).
Localization of an antithrombin exosite that promotes rapid inhibition of factors Xa and IXa dependent on heparin activation of the serpin.
  J Biol Chem, 278, 51433-51440.  
14519117 G.L.Long, M.Kjellberg, B.O.Villoutreix, and J.Stenflo (2003).
Probing plasma clearance of the thrombin-antithrombin complex with a monoclonal antibody against the putative serpin-enzyme complex receptor-binding site.
  Eur J Biochem, 270, 4059-4069.  
12556442 M.A.Jairajpuri, A.Lu, U.Desai, S.T.Olson, I.Bjork, and S.C.Bock (2003).
Antithrombin III phenylalanines 122 and 121 contribute to its high affinity for heparin and its conformational activation.
  J Biol Chem, 278, 15941-15950.  
12606560 N.V.Gorlatova, H.Elokdah, K.Fan, D.L.Crandall, and D.A.Lawrence (2003).
Mapping of a conformational epitope on plasminogen activator inhibitor-1 by random mutagenesis. Implications for serpin function.
  J Biol Chem, 278, 16329-16335.  
12591924 S.M.Raja, N.Chhablani, R.Swanson, E.Thompson, M.Laffan, D.A.Lane, and S.T.Olson (2003).
Deletion of P1 arginine in a novel antithrombin variant (antithrombin London) abolishes inhibitory activity but enhances heparin affinity and is associated with early onset thrombosis.
  J Biol Chem, 278, 13688-13695.  
12694181 T.Wind, J.K.Jensen, D.M.Dupont, P.Kulig, and P.A.Andreasen (2003).
Mutational analysis of plasminogen activator inhibitor-1.
  Eur J Biochem, 270, 1680-1688.  
11741963 K.J.Belzar, A.Zhou, R.W.Carrell, P.G.Gettins, and J.A.Huntington (2002).
Helix D elongation and allosteric activation of antithrombin.
  J Biol Chem, 277, 8551-8558.  
11971909 M.A.Jairajpuri, A.Lu, and S.C.Bock (2002).
Elimination of P1 arginine 393 interaction with underlying glutamic acid 255 partially activates antithrombin III for thrombin inhibition but not factor Xa inhibition.
  J Biol Chem, 277, 24460-24465.  
11806943 M.P.McGee, J.Liang, and J.Luba (2002).
Hydration effects of heparin on antithrombin probed by osmotic stress.
  Biophys J, 82, 1040-1049.  
11854268 N.S.Quinsey, J.C.Whisstock, B.Le Bonniec, V.Louvain, S.P.Bottomley, and R.N.Pike (2002).
Molecular determinants of the mechanism underlying acceleration of the interaction between antithrombin and factor Xa by heparin pentasaccharide.
  J Biol Chem, 277, 15971-15978.  
12023970 S.Janciauskiene, R.Dominaitiene, N.H.Sternby, E.Piitulainen, and S.Eriksson (2002).
Detection of circulating and endothelial cell polymers of Z and wild type alpha 1-antitrypsin by a monoclonal antibody.
  J Biol Chem, 277, 26540-26546.  
11891340 S.M.Prince, M.Achtman, and J.P.Derrick (2002).
Crystal structure of the OpcA integral membrane adhesin from Neisseria meningitidis.
  Proc Natl Acad Sci U S A, 99, 3417-3421.
PDB code: 1k24
11939772 S.Schedin-Weiss, U.R.Desai, S.C.Bock, P.G.Gettins, S.T.Olson, and I.Björk (2002).
Importance of lysine 125 for heparin binding and activation of antithrombin.
  Biochemistry, 41, 4779-4788.  
  12466122 Y.Cao, A.Lundwall, V.Gadaleanu, H.Lilja, and A.Bjartell (2002).
Anti-thrombin is expressed in the benign prostatic epithelium and in prostate cancer and is capable of forming complexes with prostate-specific antigen and human glandular kallikrein 2.
  Am J Pathol, 161, 2053-2063.  
12399451 Y.Tanaka, K.Ueda, T.Ozawa, N.Sakuragawa, S.Yokota, R.Sato, S.Okamura, M.Morita, and T.Imanaka (2002).
Intracellular accumulation of antithrombin Morioka (C95R), a novel mutation causing type I antithrombin deficiency.
  J Biol Chem, 277, 51058-51067.  
11159419 J.P.Ludeman, J.C.Whisstock, P.C.Hopkins, B.F.Le Bonniec, and S.P.Bottomley (2001).
Structure of a serpin-enzyme complex probed by cysteine substitutions and fluorescence spectroscopy.
  Biophys J, 80, 491-497.  
11445465 L.J.DeLucas (2001).
Protein crystallization - is it rocket science?
  Drug Discov Today, 6, 734-744.  
11805532 S.M.Opal (2001).
Clinical impact of novel anticoagulation strategies in sepsis.
  Curr Opin Crit Care, 7, 347-353.  
11714919 S.P.Bottomley, I.D.Lawrenson, D.Tew, W.Dai, J.C.Whisstock, and R.N.Pike (2001).
The role of strand 1 of the C beta-sheet in the structure and function of alpha(1)-antitrypsin.
  Protein Sci, 10, 2518-2524.  
11567021 V.Arocas, S.C.Bock, S.Raja, S.T.Olson, and I.Bjork (2001).
Lysine 114 of antithrombin is of crucial importance for the affinity and kinetics of heparin pentasaccharide binding.
  J Biol Chem, 276, 43809-43817.  
10660568 A.Futamura, and P.G.Gettins (2000).
Serine 380 (P14) --> glutamate mutation activates antithrombin as an inhibitor of factor Xa.
  J Biol Chem, 275, 4092-4098.  
11101304 E.Doss-Pepe, P.Deprez, N.C.Inestrosa, and B.Brodsky (2000).
Interaction of collagen-like peptide models of asymmetric acetylcholinesterase with glycosaminoglycans: spectroscopic studies of conformational changes and stability.
  Biochemistry, 39, 14884-14892.  
10644732 J.L.Meagher, S.T.Olson, and P.G.Gettins (2000).
Critical role of the linker region between helix D and strand 2A in heparin activation of antithrombin.
  J Biol Chem, 275, 2698-2704.  
  10933492 P.R.Elliott, X.Y.Pei, T.R.Dafforn, and D.A.Lomas (2000).
Topography of a 2.0 A structure of alpha1-antitrypsin reveals targets for rational drug design to prevent conformational disease.
  Protein Sci, 9, 1274-1281.
PDB code: 1qlp
11087944 Y.Hayakawa, T.Hayashi, J.Lee, P.Srisomporn, M.Maeda, T.Ozawa, and N.Sakuragawa (2000).
Inhibition of thrombin by sulfated polysaccharides isolated from green algae.
  Biochim Biophys Acta, 1543, 86-94.  
10380350 A.Lombardi, G.De Simone, S.Galdiero, N.Staiano, F.Nastri, and V.Pavone (1999).
From natural to synthetic multisite thrombin inhibitors.
  Biopolymers, 51, 19-39.  
10215897 M.Hricovíni, M.Guerrini, and A.Bisio (1999).
Structure of heparin-derived tetrasaccharide complexed to the plasma protein antithrombin derived from NOEs, J-couplings and chemical shifts.
  Eur J Biochem, 261, 789-801.  
10092640 T.R.Dafforn, R.Mahadeva, P.R.Elliott, P.Sivasothy, and D.A.Lomas (1999).
A kinetic mechanism for the polymerization of alpha1-antitrypsin.
  J Biol Chem, 274, 9548-9555.  
9988693 V.Picard, P.E.Marque, F.Paolucci, M.Aiach, and B.F.Le Bonniec (1999).
Topology of the stable serpin-protease complexes revealed by an autoantibody that fails to react with the monomeric conformers of antithrombin.
  J Biol Chem, 274, 4586-4593.  
10364215 Y.Luo, Y.Zhou, and B.S.Cooperman (1999).
Antichymotrypsin interaction with chymotrypsin. Intermediates on the way to inhibited complex formation.
  J Biol Chem, 274, 17733-17741.  
9808033 C.T.Esmon, and T.Mather (1998).
Switching serine protease specificity.
  Nat Struct Biol, 5, 933-937.  
9692954 E.Alberdi, C.C.Hyde, and S.P.Becerra (1998).
Pigment epithelium-derived factor (PEDF) binds to glycosaminoglycans: analysis of the binding site.
  Biochemistry, 37, 10643-10652.  
  9541411 H.L.Fitton, R.Skinner, T.R.Dafforn, L.Jin, and R.N.Pike (1998).
The N-terminal segment of antithrombin acts as a steric gate for the binding of heparin.
  Protein Sci, 7, 782-788.  
9722560 J.L.Meagher, J.M.Beechem, S.T.Olson, and P.G.Gettins (1998).
Deconvolution of the fluorescence emission spectrum of human antithrombin and identification of the tryptophan residues that are responsive to heparin binding.
  J Biol Chem, 273, 23283-23289.  
9538691 J.Whisstock, R.Skinner, and A.M.Lesk (1998).
An atlas of serpin conformations.
  Trends Biochem Sci, 23, 63-67.  
9774414 L.Zhang, J.J.Schwartz, J.Miller, J.Liu, L.M.Fritze, N.W.Shworak, and R.D.Rosenberg (1998).
The retinoic acid and cAMP-dependent up-regulation of 3-O-sulfotransferase-1 leads to a dramatic augmentation of anticoagulantly active heparan sulfate biosynthesis in F9 embryonal carcinoma cells.
  J Biol Chem, 273, 27998-28003.  
9477948 P.Björquist, J.Ehnebom, T.Inghardt, L.Hansson, M.Lindberg, M.Linschoten, M.Strömqvist, and J.Deinum (1998).
Identification of the binding site for a low-molecular-weight inhibitor of plasminogen activator inhibitor type 1 by site-directed mutagenesis.
  Biochemistry, 37, 1227-1234.  
9740326 S.Jansen, R.Jones, I.Jenneckens, B.Marschall, B.Kriegesmann, J.Coadwell, and B.Brenig (1998).
Site-directed mutagenesis of boar proacrosin reveals residues involved in binding of zona pellucida glycoproteins.
  Mol Reprod Dev, 51, 184-192.  
9452500 W.S.Chang, and D.A.Lomas (1998).
Latent alpha1-antichymotrypsin. A molecular explanation for the inactivation of alpha1-antichymotrypsin in chronic bronchitis and emphysema.
  J Biol Chem, 273, 3695-3701.  
9634700 Y.Xue, P.Björquist, T.Inghardt, M.Linschoten, D.Musil, L.Sjölin, and J.Deinum (1998).
Interfering with the inhibitory mechanism of serpins: crystal structure of a complex formed between cleaved plasminogen activator inhibitor type 1 and a reactive-centre loop peptide.
  Structure, 6, 627-636.
PDB code: 1a7c
9235938 E.Ersdal-Badju, A.Lu, Y.Zuo, V.Picard, and S.C.Bock (1997).
Identification of the antithrombin III heparin binding site.
  J Biol Chem, 272, 19393-19400.  
  9385643 G.Pujadas, and J.Palau (1997).
Anatomy of a conformational transition of beta-strand 6 in soybean beta-amylase caused by substrate (or inhibitor) binding to the catalytical site.
  Protein Sci, 6, 2409-2417.  
  9348117 H.L.Fitton, R.N.Pike, R.W.Carrell, and W.S.Chang (1997).
Mechanisms of antithrombin polymerisation and heparin activation probed by the insertion of synthetic reactive loop peptides.
  Biol Chem, 378, 1059-1063.  
9405673 L.Jin, J.P.Abrahams, R.Skinner, M.Petitou, R.N.Pike, and R.W.Carrell (1997).
The anticoagulant activation of antithrombin by heparin.
  Proc Natl Acad Sci U S A, 94, 14683-14688.
PDB code: 1azx
9335576 M.R.Wardell, W.S.Chang, D.Bruce, R.Skinner, A.M.Lesk, and R.W.Carrell (1997).
Preparative induction and characterization of L-antithrombin: a structural homologue of latent plasminogen activator inhibitor-1.
  Biochemistry, 36, 13133-13142.  
9242619 R.N.Pike, J.Potempa, R.Skinner, H.L.Fitton, W.T.McGraw, J.Travis, M.Owen, L.Jin, and R.W.Carrell (1997).
Heparin-dependent modification of the reactive center arginine of antithrombin and consequent increase in heparin binding affinity.
  J Biol Chem, 272, 19652-19655.  
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.