PDBsum entry 1jmj

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Blood clotting PDB id
Protein chains
397 a.a. *
Waters ×297
* Residue conservation analysis
PDB id:
Name: Blood clotting
Title: Crystal structure of native heparin cofactor ii
Structure: Heparin cofactor ii. Chain: a, b. Synonym: hc-ii. Protease inhibitor leuserpin 2. Hls2. Serin cysteine) proteinase inhibitor, clade d (heparin cofactor),
Source: Homo sapiens. Human. Organism_taxid: 9606
Biol. unit: Dimer (from PQS)
2.35Å     R-factor:   0.208     R-free:   0.255
Authors: T.P.Baglin,R.W.Carrell,F.C.Church,J.A.Huntington
Key ref:
T.P.Baglin et al. (2002). Crystal structures of native and thrombin-complexed heparin cofactor II reveal a multistep allosteric mechanism. Proc Natl Acad Sci U S A, 99, 11079-11084. PubMed id: 12169660 DOI: 10.1073/pnas.162232399
18-Jul-01     Release date:   30-Aug-02    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P05546  (HEP2_HUMAN) -  Heparin cofactor 2
499 a.a.
397 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     hemostasis   6 terms 
  Biochemical function     peptidase inhibitor activity     4 terms  


DOI no: 10.1073/pnas.162232399 Proc Natl Acad Sci U S A 99:11079-11084 (2002)
PubMed id: 12169660  
Crystal structures of native and thrombin-complexed heparin cofactor II reveal a multistep allosteric mechanism.
T.P.Baglin, R.W.Carrell, F.C.Church, C.T.Esmon, J.A.Huntington.
The serine proteases sequentially activated to form a fibrin clot are inhibited primarily by members of the serpin family, which use a unique beta-sheet expansion mechanism to trap and destroy their targets. Since the discovery that serpins were a family of serine protease inhibitors there has been controversy as to the role of conformational change in their mechanism. It now is clear that protease inhibition depends entirely on rapid serpin beta-sheet expansion after proteolytic attack. The regulatory advantage afforded by the conformational mobility of serpins is demonstrated here by the structures of native and S195A thrombin-complexed heparin cofactor II (HCII). HCII inhibits thrombin, the final protease of the coagulation cascade, in a glycosaminoglycan-dependent manner that involves the release of a sequestered hirudin-like N-terminal tail for interaction with thrombin. The native structure of HCII resembles that of native antithrombin and suggests an alternative mechanism of allosteric activation, whereas the structure of the S195A thrombin-HCII complex defines the molecular basis of allostery. Together, these structures reveal a multistep allosteric mechanism that relies on sequential contraction and expansion of the central beta-sheet of HCII.
  Selected figure(s)  
Figure 2.
Fig 2. Crystallographic structure of the HCII-thrombin Michaelis complex. (a) A stereo representation of the Michaelis complex between S195A thrombin (cyan) and HCII (colored as described for Fig. 1), with the -loop in front and the 60-insertion loop behind the reactive center loop. (b) Stereo representation of the electron density covering the portion of the acidic tail (yellow) that interacts with thrombin (magenta), contoured at 1 . (c) The subsite interactions between the reactive center residues of HCII (rods) and the active site cleft of thrombin (surface representation) are extensive and complementary in both electrostatic (Left, negative potential is red, and positive is blue) and hydrophobic (Right, green for hydrophobic side chains) properties. (d) The interaction between exosite I of thrombin (surface representation as described for c) and the hirudin-like N-terminal tail of HCII (rods, the side chains of residues not interacting with thrombin were removed for clarity) is primarily hydrophobic. The only ionic interactions are between Asp-70 and Asp-72 of HCII and L110H of thrombin. Sulfated tyrosines, 60 and 73, make no contacts with thrombin and are not shown.
Figure 3.
Fig 3. The sequential mechanism of GAG-mediated thrombin inhibition by HCII (as described in Results and Discussion). For a video of this mechanism, see Movie 2.
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21465556 C.An, S.Lovell, M.R.Kanost, K.P.Battaile, and K.Michel (2011).
Crystal structure of native Anopheles gambiae serpin-2, a negative regulator of melanization in mosquitoes.
  Proteins, 79, 1999-2003.
PDB code: 3pzf
  20835364 A.Raghuraman, P.D.Mosier, and U.R.Desai (2010).
Understanding Dermatan Sulfate-Heparin Cofactor II Interaction through Virtual Library Screening.
  ACS Med Chem Lett, 1, 281-285.  
20731544 J.A.Huntington, and J.C.Whisstock (2010).
Molecular contortionism - on the physical limits of serpin 'loop-sheet' polymers.
  Biol Chem, 391, 973-982.  
20053992 S.Sarilla, S.Y.Habib, D.V.Kravtsov, A.Matafonov, D.Gailani, and I.M.Verhamme (2010).
Sucrose octasulfate selectively accelerates thrombin inactivation by heparin cofactor II.
  J Biol Chem, 285, 8278-8289.  
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
19343519 B.Mickowska (2009).
Purification and characterization of alpha(1)-proteinase inhibitor and antithrombin III: major serpins of rainbow trout (Oncorhynchuss mykiss) and carp (Cyprinus carpio) blood plasma.
  Fish Physiol Biochem, 35, 231-240.  
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.  
19849829 M.Garrett, A.Fullaondo, L.Troxler, G.Micklem, and D.Gubb (2009).
Identification and analysis of serpin-family genes by homology and synteny across the 12 sequenced Drosophilid genomes.
  BMC Genomics, 10, 489.  
19589779 N.S.Petrera, A.R.Stafford, B.A.Leslie, C.A.Kretz, J.C.Fredenburgh, and J.I.Weitz (2009).
Long range communication between exosites 1 and 2 modulates thrombin function.
  J Biol Chem, 284, 25620-25629.  
19401470 P.G.Gettins, and S.T.Olson (2009).
Exosite determinants of serpin specificity.
  J Biol Chem, 284, 20441-20445.  
19656282 T.E.Adams, W.Li, and J.A.Huntington (2009).
Molecular basis of thrombomodulin activation of slow thrombin.
  J Thromb Haemost, 7, 1688-1695.
PDB code: 3gis
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.  
18329094 E.Di Cera (2008).
  Mol Aspects Med, 29, 203-254.  
18156656 S.A.Osborne, R.A.Daniel, K.Desilva, and R.B.Seymour (2008).
Antithrombin activity and disaccharide composition of dermatan sulfate from different bovine tissues.
  Glycobiology, 18, 225-234.  
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.  
18060440 T.H.Roberts, and J.Hejgaard (2008).
Serpins in plants and green algae.
  Funct Integr Genomics, 8, 1.  
18362344 W.Li, T.E.Adams, J.Nangalia, C.T.Esmon, and J.A.Huntington (2008).
Molecular basis of thrombin recognition by protein C inhibitor revealed by the 1.6-A structure of the heparin-bridged complex.
  Proc Natl Acad Sci U S A, 105, 4661-4666.
PDB code: 3b9f
17347701 E.Di Cera, M.J.Page, A.Bah, L.A.Bush-Pelc, and L.C.Garvey (2007).
Thrombin allostery.
  Phys Chem Chem Phys, 9, 1291-1306.  
17635727 E.Di Cera (2007).
Thrombin as procoagulant and anticoagulant.
  J Thromb Haemost, 5, 196-202.  
17635716 J.C.Rau, L.M.Beaulieu, J.A.Huntington, and F.C.Church (2007).
Serpins in thrombosis, hemostasis and fibrinolysis.
  J Thromb Haemost, 5, 102-115.  
17982317 T.Taketomi, F.Szlam, J.Vinten-Johansen, J.H.Levy, and K.A.Tanaka (2007).
Thrombin-activated thrombelastography for evaluation of thrombin interaction with thrombin inhibitors.
  Blood Coagul Fibrinolysis, 18, 761-767.  
17214598 D.A.Lauver, and B.R.Lucchesi (2006).
Sulodexide: a renewed interest in this glycosaminoglycan.
  Cardiovasc Drug Rev, 24, 214-226.  
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.  
16527896 J.Corral, R.González-Conejero, J.M.Soria, J.R.González-Porras, E.Pérez-Ceballos, R.Lecumberri, V.Roldán, J.C.Souto, A.Miñano, D.Hernández-Espinosa, I.Alberca, J.Fontcuberta, and V.Vicente (2006).
A nonsense polymorphism in the protein Z-dependent protease inhibitor increases the risk for venous thrombosis.
  Blood, 108, 177-183.  
16360948 N.Pelte, A.S.Robertson, Z.Zou, D.Belorgey, T.R.Dafforn, H.Jiang, D.Lomas, J.M.Reichhart, and D.Gubb (2006).
Immune challenge induces N-terminal cleavage of the Drosophila serpin Necrotic.
  Insect Biochem Mol Biol, 36, 37-46.  
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.  
16810322 S.McGowan, A.M.Buckle, J.A.Irving, P.C.Ong, T.A.Bashtannyk-Puhalovich, W.T.Kan, K.N.Henderson, Y.A.Bulynko, E.Y.Popova, A.I.Smith, S.P.Bottomley, J.Rossjohn, S.A.Grigoryev, R.N.Pike, and J.C.Whisstock (2006).
X-ray crystal structure of MENT: evidence for functional loop-sheet polymers in chromatin condensation.
  EMBO J, 25, 3144-3155.
PDB codes: 2dut 2h4p 2h4q 2h4r 2h4s
16281932 C.T.Esmon (2005).
The interactions between inflammation and coagulation.
  Br J Haematol, 131, 417-430.  
16102053 J.A.Huntington (2005).
Molecular recognition mechanisms of thrombin.
  J Thromb Haemost, 3, 1861-1872.  
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.  
15892855 W.Bode (2005).
The structure of thrombin, a chameleon-like proteinase.
  J Thromb Haemost, 3, 2379-2388.  
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
15364056 C.T.Esmon (2004).
Interactions between the innate immune and blood coagulation systems.
  Trends Immunol, 25, 536-542.  
15461625 N.Van de Water, T.Tan, F.Ashton, A.O'Grady, T.Day, P.Browett, P.Ockelford, and P.Harper (2004).
Mutations within the protein Z-dependent protease inhibitor gene are associated with venous thromboembolic disease: a new form of thrombophilia.
  Br J Haematol, 127, 190-194.  
15511233 S.Brinkmeyer, R.Eckert, and H.Ragg (2004).
Reformable intramolecular cross-linking of the N-terminal domain of heparin cofactor II: effects on enzyme inhibition.
  Eur J Biochem, 271, 4275-4283.  
14705167 U.R.Desai (2004).
New antithrombin-based anticoagulants.
  Med Res Rev, 24, 151-181.  
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
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.  
12871289 J.A.Huntington (2003).
Mechanisms of glycosaminoglycan activation of the serpins in hemostasis.
  J Thromb Haemost, 1, 1535-1549.  
14607082 J.A.Huntington, and T.P.Baglin (2003).
Targeting thrombin--rational drug design from natural mechanisms.
  Trends Pharmacol Sci, 24, 589-595.  
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.