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PDBsum entry 2sge
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protein ligands metals Protein-protein interface(s) links
Hydrolase/hydrolase inhibitor PDB id
2sge

 

 

 

 

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Contents
Protein chains
185 a.a. *
51 a.a. *
Ligands
PO4
Metals
__K
Waters ×151
* Residue conservation analysis
PDB id:
2sge
Name: Hydrolase/hydrolase inhibitor
Title: Glu 18 variant of turkey ovomucoid inhibitor third domain complexed with streptomyces griseus proteinase b at ph 10.7
Structure: Streptogrisin b. Chain: e. Synonym: protease b, sgpb, pronase enzyme b. Ovomucoid. Chain: i. Fragment: third domain. Synonym: glu18-omtky3. Engineered: yes. Mutation: yes
Source: Streptomyces griseus. Organism_taxid: 1911. Strain: k1. Meleagris gallopavo. Turkey. Organism_taxid: 9103. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.198    
Authors: K.Huang,W.Lu,S.Anderson,M.Laskowski Jr.,M.N.G.James
Key ref: K.Huang et al. (1995). Water molecules participate in proteinase-inhibitor interactions: crystal structures of Leu18, Ala18, and Gly18 variants of turkey ovomucoid inhibitor third domain complexed with Streptomyces griseus proteinase B. Protein Sci, 4, 1985-1997. PubMed id: 8535235 DOI: 10.1002/pro.5560041004
Date:
25-Mar-99     Release date:   26-Aug-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00777  (PRTB_STRGR) -  Streptogrisin-B from Streptomyces griseus
Seq:
Struc: 		299 a.a.
185 a.a.
Protein chain
Pfam   ArchSchema ?
P68390  (IOVO_MELGA) -  Ovomucoid from Meleagris gallopavo
Seq:
Struc: 		185 a.a.
51 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chain E: E.C.3.4.21.81  - streptogrisin B.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of proteins with specificity similar to trypsin.

 

 
DOI no: 10.1002/pro.5560041004 Protein Sci 4:1985-1997 (1995)
PubMed id: 8535235  
 
 
Water molecules participate in proteinase-inhibitor interactions: crystal structures of Leu18, Ala18, and Gly18 variants of turkey ovomucoid inhibitor third domain complexed with Streptomyces griseus proteinase B.
K.Huang, W.Lu, S.Anderson, M.Laskowski, M.N.James.
 
  ABSTRACT  
 
Crystal structures of the complexes of Streptomyces griseus proteinase B (SGPB) with three P1 variants of turkey ovomucoid inhibitor third domain (OMTKY3), Leu18, Ala18, and Gly18, have been determined and refined to high resolution. Comparisons among these structures and of each with native, uncomplexed SGPB reveal that each complex features a unique solvent structure in the S1 binding pocket. The number and relative positions of water molecules bound in the S1 binding pocket vary according to the size of the side chain of the P1 residue. Water molecules in the S1 binding pocket of SGPB are redistributed in response to the complex formation, probably to optimize hydrogen bonds between the enzyme and the inhibitor. There are extensive water-mediated hydrogen bonds in the interfaces of the complexes. In all complexes, Asn 36 of OMTKY3 participates in forming hydrogen bonds, via water molecules, with residues lining the S1 binding pocket of SGPB. For a homologous series of aliphatic straight side chains, Gly18, Ala18, Abu18, Ape18, and Ahp18 variants, the binding free energy is a linear function of the hydrophobic surface area buried in the interface of the corresponding complexes. The resulting constant of proportionality is 34.1 cal mol-1 A-2. These structures confirm that the binding of OMTKY3 to the preformed S1 pocket in SGPB involves no substantial structural disturbances that commonly occur in the site-directed mutagenesis studies of interior residues in other proteins, thus providing one of the most reliable assessments of the contribution of the hydrophobic effect to protein-complex stability.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20831336 B.Kim, J.Song, and X.Song (2010).
Calculations of the binding affinities of protein-protein complexes with the fast multipole method.
  J Chem Phys, 133, 095101.  
18795369 Y.Li, Y.Q.Qian, W.M.Ma, and W.J.Yang (2009).
Inhibition mechanism and the effects of structure on activity of male reproduction-related peptidase inhibitor Kazal-type (MRPINK) of Macrobrachium rosenbergii.
  Mar Biotechnol (NY), 11, 252-259.  
17242738 Z.Li, and T.Lazaridis (2007).
Water at biomolecular binding interfaces.
  Phys Chem Chem Phys, 9, 573-581.  
16752417 B.O.Brandsdal, A.O.Smalås, and J.Aqvist (2006).
Free energy calculations show that acidic P1 variants undergo large pKa shifts upon binding to trypsin.
  Proteins, 64, 740-748.  
16272444 M.Almlöf, J.Aqvist, A.O.Smalås, and B.O.Brandsdal (2006).
Probing the effect of point mutations at protein-protein interfaces with free energy calculations.
  Biophys J, 90, 433-442.  
16905103 M.Renatus, S.G.Parrado, A.D'Arcy, U.Eidhoff, B.Gerhartz, U.Hassiepen, B.Pierrat, R.Riedl, D.Vinzenz, S.Worpenberg, and M.Kroemer (2006).
Structural basis of ubiquitin recognition by the deubiquitinating protease USP2.
  Structure, 14, 1293-1302.
PDB code: 2hd5
15856483 F.Rodier, R.P.Bahadur, P.Chakrabarti, and J.Janin (2005).
Hydration of protein-protein interfaces.
  Proteins, 60, 36-45.  
15858268 J.T.Maynes, M.M.Cherney, M.A.Qasim, M.Laskowski, and M.N.James (2005).
Structure of the subtilisin Carlsberg-OMTKY3 complex reveals two different ovomucoid conformations.
  Acta Crystallogr D Biol Crystallogr, 61, 580-588.
PDB code: 1yu6
15139817 B.Jayaram, and T.Jain (2004).
The role of water in protein-DNA recognition.
  Annu Rev Biophys Biomol Struct, 33, 343-361.  
15152084 V.De Filippis, S.De Boni, E.De Dea, D.Dalzoppo, C.Grandi, and A.Fontana (2004).
Incorporation of the fluorescent amino acid 7-azatryptophan into the core domain 1-47 of hirudin as a probe of hirudin folding and thrombin recognition.
  Protein Sci, 13, 1489-1502.  
14579354 J.Mintseris, and Z.Weng (2003).
Atomic contact vectors in protein-protein recognition.
  Proteins, 53, 629-639.  
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.  
12649444 T.T.Waldron, M.A.Modestou, and K.P.Murphy (2003).
Anion binding to a protein-protein complex lacks dependence on net charge.
  Protein Sci, 12, 871-874.  
12437101 H.Brandstetter, J.S.Kim, M.Groll, P.Göttig, and R.Huber (2002).
Structural basis for the processive protein degradation by tricorn protease.
  Biol Chem, 383, 1157-1165.  
11468355 B.O.Brandsdal, J.Aqvist, and A.O.Smalås (2001).
Computational analysis of binding of P1 variants to trypsin.
  Protein Sci, 10, 1584-1595.  
11719810 H.Brandstetter, J.S.Kim, M.Groll, and R.Huber (2001).
Crystal structure of the tricorn protease reveals a protein disassembly line.
  Nature, 414, 466-470.
PDB code: 1k32
11171964 S.M.Lu, W.Lu, M.A.Qasim, S.Anderson, I.Apostol, W.Ardelt, T.Bigler, Y.W.Chiang, J.Cook, M.N.James, I.Kato, C.Kelly, W.Kohr, T.Komiyama, T.Y.Lin, M.Ogawa, J.Otlewski, S.J.Park, S.Qasim, M.Ranjbar, M.Tashiro, N.Warne, H.Whatley, A.Wieczorek, M.Wieczorek, T.Wilusz, R.Wynn, W.Zhang, and M.Laskowski (2001).
Predicting the reactivity of proteins from their sequence alone: Kazal family of protein inhibitors of serine proteinases.
  Proc Natl Acad Sci U S A, 98, 1410-1415.  
  10739250 K.S.Bateman, S.Anderson, W.Lu, M.A.Qasim, M.Laskowski, and M.N.James (2000).
Deleterious effects of beta-branched residues in the S1 specificity pocket of Streptomyces griseus proteinase B (SGPB): crystal structures of the turkey ovomucoid third domain variants Ile18I, Val18I, Thr18I, and Ser18I in complex with SGPB.
  Protein Sci, 9, 83-94.
PDB codes: 1cso 1ct0 1ct2 1ct4
  10850802 S.P.Edgcomb, B.M.Baker, and K.P.Murphy (2000).
The energetics of phosphate binding to a protein complex.
  Protein Sci, 9, 927-933.  
10891089 W.R.Forsyth, and A.D.Robertson (2000).
Insensitivity of perturbed carboxyl pK(a) values in the ovomucoid third domain to charge replacement at a neighboring residue.
  Biochemistry, 39, 8067-8072.  
10500110 A.R.Khan, N.Khazanovich-Bernstein, E.M.Bergmann, and M.N.James (1999).
Structural aspects of activation pathways of aspartic protease zymogens and viral 3C protease precursors.
  Proc Natl Acad Sci U S A, 96, 10968-10975.  
10102985 H.Czapinska, and J.Otlewski (1999).
Structural and energetic determinants of the S1-site specificity in serine proteases.
  Eur J Biochem, 260, 571-595.  
10647173 J.Janin (1999).
Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition.
  Structure, 7, R277-R279.  
9241426 H.S.Chan, and K.A.Dill (1997).
Solvation: how to obtain microscopic energies from partitioning and solvation experiments.
  Annu Rev Biophys Biomol Struct, 26, 425-459.  
8939759 R.A.Engh, H.Brandstetter, G.Sucher, A.Eichinger, U.Baumann, W.Bode, R.Huber, T.Poll, R.Rudolph, and W.von der Saal (1996).
Enzyme flexibility, solvent and 'weak' interactions characterize thrombin-ligand interactions: implications for drug design.
  Structure, 4, 1353-1362.
PDB codes: 1uvs 1uvt 1uvu
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.

 

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