PDBsum entry 3cki

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protein metals Protein-protein interface(s) links
Hydrolase, hydrolase inhibitor PDB id
Protein chains
256 a.a. *
121 a.a. *
Waters ×190
* Residue conservation analysis
PDB id:
Name: Hydrolase, hydrolase inhibitor
Title: Crystal structure of the tace-n-timp-3 complex
Structure: Adam 17. Chain: a. Fragment: tace catalytic domain (unp residues 219-474). Synonym: a disintegrin and metalloproteinase domain 17, tnf-alpha-converting enzyme, tnf-alpha convertase, snake venom-like protease, cd156b antigen. Engineered: yes. Mutation: yes. Metalloproteinase inhibitor 3.
Source: Homo sapiens. Human. Gene: adam17, csvp, tace. Expressed in: cricetulus griseus. Expression_system_cell_line: cho. Expression_system_organ: ovary. Gene: timp3. Expressed in: escherichia coli
2.30Å     R-factor:   0.234     R-free:   0.284
Authors: M.Wisniewska,P.Goettig,K.Maskos,E.Belouski,D.Winters, R.Hecht,R.Black,W.Bode
Key ref:
M.Wisniewska et al. (2008). Structural determinants of the ADAM inhibition by TIMP-3: crystal structure of the TACE-N-TIMP-3 complex. J Mol Biol, 381, 1307-1319. PubMed id: 18638486 DOI: 10.1016/j.jmb.2008.06.088
15-Mar-08     Release date:   05-Aug-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P78536  (ADA17_HUMAN) -  Disintegrin and metalloproteinase domain-containing protein 17
824 a.a.
256 a.a.*
Protein chain
Pfam   ArchSchema ?
P35625  (TIMP3_HUMAN) -  Metalloproteinase inhibitor 3
211 a.a.
121 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chain A: E.C.  - Adam 17 endopeptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Cofactor: Zn(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     metalloendopeptidase inhibitor activity     3 terms  


DOI no: 10.1016/j.jmb.2008.06.088 J Mol Biol 381:1307-1319 (2008)
PubMed id: 18638486  
Structural determinants of the ADAM inhibition by TIMP-3: crystal structure of the TACE-N-TIMP-3 complex.
M.Wisniewska, P.Goettig, K.Maskos, E.Belouski, D.Winters, R.Hecht, R.Black, W.Bode.
TIMP-3 (tissue inhibitor of metalloproteinases 3) is unique among the TIMP inhibitors, in that it effectively inhibits the TNF-alpha converting enzyme (TACE). In order to understand this selective capability of inhibition, we crystallized the complex formed by the catalytic domain of recombinant human TACE and the N-terminal domain of TIMP-3 (N-TIMP-3), and determined its molecular structure with X-ray data to 2.3 A resolution. The structure reveals that TIMP-3 exhibits a fold similar to those of TIMP-1 and TIMP-2, and interacts through its functional binding edge, which consists of the N-terminal segment and other loops, with the active-site cleft of TACE in a manner similar to that of matrix metalloproteinases (MMPs). Therefore, the mechanism of TIMP-3 binding toward TACE is not fundamentally different from that previously elucidated for the MMPs. The Phe34 phenyl side chain situated at the tip of the relatively short sA-sB loop of TIMP-3 extends into a unique hydrophobic groove of the TACE surface, and two Leu residues in the adjacent sC-connector and sE-sF loops are tightly packed in the interface allowing favourable interactions, in agreement with predictions obtained by systematic mutations by Gillian Murphy's group. The combination of favourable functional epitopes together with a considerable flexibility renders TIMP-3 an efficient TACE inhibitor. This structure might provide means to design more efficient TIMP inhibitors of TACE.
  Selected figure(s)  
Figure 1.
Fig. 1. Stereo front view of the cdTACE*N-TIMP-3 complex (green ribbon, catalytic domain; orange ribbon, N-TIMP-3; pink sphere, catalytic zinc). Helices, strands and selected loops of cdTACE and N-TIMP-3 are labelled. All disulfide bridges, exposed residues at the N-terminal segment (Cys1, Thr2, Cys3, Ser4, Pro5, Ser6) and in loops playing an important role in enzyme binding (Pro33, Phe34, Ser66, Leu67, Leu94), as well as the Lys residues of N-TIMP-3 known to be involved in ECM binding (Lys26, 27, 30, and 76^30) and some TACE residues lining the hydrophobic groove accommodating the sA-sB loop are shown as stick models.
Figure 3.
Fig. 3. Comparison of the intermolecular interactions in the cdTACE*N-TIMP-3 and in the cdMMP-3*TIMP-1^17 complex. The view is from the inhibitor moieties (orange and green stick models, with oxygen atoms in red, nitrogen atoms in blue, and sulphur atoms in yellow) towards the active-site clefts of cdTACE and cdMMP (standard view, related to the front view of Fig. 1 by a 90° rotation around x), with the enzymes represented by rigid surfaces calculated without the catalytic zinc and coloured according to the electrostatic potential. The catalytic zinc ions are shown as pink spheres. (a) Only N-TIMP-3 segments Pro33-Phe34, Glu65-Cys68, Leu94-Cys95, and Cys1-Ser4 are given with all non-hydrogen atoms, to show the tightly packed Cys1 N-terminus, and the nestling of Phe34, Leu67 and Leu94 into hydrophobic grooves. (b) TIMP-1 segments Tyr35, Glu67-Cys70, Thr98-Cys99, and Cys1-Val4 (TIMP-1 nomenclature) are displayed with all non-hydrogen atoms, to highlight the tight packing of the Cys1 N-terminus and the nestling of Val69 and Thr98 towards the complementary hydrophobic surfaces.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 381, 1307-1319) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21352830 K.Kucera, L.M.Harrison, M.Cappello, and Y.Modis (2011).
Ancylostoma ceylanicum excretory-secretory protein 2 adopts a netrin-like fold and defines a novel family of nematode proteins.
  J Mol Biol, 408, 9.
PDB code: 3nsw
20628198 A.Murthy, V.Defamie, D.S.Smookler, M.A.Di Grappa, K.Horiuchi, M.Federici, M.Sibilia, C.P.Blobel, and R.Khokha (2010).
Ectodomain shedding of EGFR ligands and TNFR1 dictates hepatocyte apoptosis during fulminant hepatitis in mice.
  J Clin Invest, 120, 2731-2744.  
20080133 K.Brew, and H.Nagase (2010).
The tissue inhibitors of metalloproteinases (TIMPs): an ancient family with structural and functional diversity.
  Biochim Biophys Acta, 1803, 55-71.  
20207734 M.Bekhouche, D.Kronenberg, S.Vadon-Le Goff, C.Bijakowski, N.H.Lim, B.Font, E.Kessler, A.Colige, H.Nagase, G.Murphy, D.J.Hulmes, and C.Moali (2010).
Role of the netrin-like domain of procollagen C-proteinase enhancer-1 in the control of metalloproteinase activity.
  J Biol Chem, 285, 15950-15959.  
20184396 M.Gooz (2010).
ADAM-17: the enzyme that does it all.
  Crit Rev Biochem Mol Biol, 45, 146-169.  
20533908 M.Kveiborg, J.Jacobsen, M.H.Lee, H.Nagase, U.M.Wewer, and G.Murphy (2010).
Selective inhibition of ADAM12 catalytic activity through engineering of tissue inhibitor of metalloproteinase 2 (TIMP-2).
  Biochem J, 430, 79-86.  
20645923 N.H.Lim, M.Kashiwagi, R.Visse, J.Jones, J.J.Enghild, K.Brew, and H.Nagase (2010).
Reactive-site mutants of N-TIMP-3 that selectively inhibit ADAMTS-4 and ADAMTS-5: biological and structural implications.
  Biochem J, 431, 113-122.  
19404668 B.Zhang, Z.Zhou, H.Lin, X.Lv, J.Fu, P.Lin, C.Zhu, and H.Wang (2009).
Protein phosphatase 1A (PPM1A) is involved in human cytotrophoblast cell invasion and migration.
  Histochem Cell Biol, 132, 169-179.  
20034386 G.Paulissen, N.Rocks, M.M.Gueders, C.Crahay, F.Quesada-Calvo, S.Bekaert, J.Hacha, M.El Hour, J.M.Foidart, A.Noel, and D.D.Cataldo (2009).
Role of ADAM and ADAMTS metalloproteinases in airway diseases.
  Respir Res, 10, 127.  
19933155 J.Guinea-Viniegra, R.Zenz, H.Scheuch, D.Hnisz, M.Holcmann, L.Bakiri, H.B.Schonthaler, M.Sibilia, and E.F.Wagner (2009).
TNFalpha shedding and epidermal inflammation are controlled by Jun proteins.
  Genes Dev, 23, 2663-2674.  
19643179 L.Troeberg, K.Fushimi, S.D.Scilabra, H.Nakamura, V.Dive, I.B.Thøgersen, J.J.Enghild, and H.Nagase (2009).
The C-terminal domains of ADAMTS-4 and ADAMTS-5 promote association with N-TIMP-3.
  Matrix Biol, 28, 463-469.  
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.