spacer
spacer

PDBsum entry 3bx1
Go to PDB code: 
protein metals Protein-protein interface(s) links
Hydrolase/hydrolase inhibitor PDB id
3bx1

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
269 a.a. *
181 a.a. *
Metals
_NA ×6
_CL ×24
_CA ×4
Waters ×574
* Residue conservation analysis
PDB id:
3bx1
Name: Hydrolase/hydrolase inhibitor
Title: Complex between the barley alpha-amylase/subtilisin inhibitor and the subtilisin savinase
Structure: Subtilisin savinase. Chain: a, b. Synonym: alkaline protease. Engineered: yes. Alpha-amylase/subtilisin inhibitor. Chain: d, c. Synonym: basi. Engineered: yes
Source: Bacillus lentus. Expressed in: bacillus subtilis. Hordeum vulgare. Barley. Expressed in: pichia pastoris
Resolution:
1.85Å     R-factor:   0.204     R-free:   0.239
Authors: P.O.Micheelsen,J.Vevodova,K.Wilson,M.Skjot
Key ref:
P.O.Micheelsen et al. (2008). Structural and mutational analyses of the interaction between the barley alpha-amylase/subtilisin inhibitor and the subtilisin savinase reveal a novel mode of inhibition. J Mol Biol, 380, 681-690. PubMed id: 18556023 DOI: 10.1016/j.jmb.2008.05.034
Date:
11-Jan-08     Release date:   08-Jul-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P29600  (SUBS_LEDLE) -  Subtilisin Savinase from Lederbergia lenta
Seq:
Struc: 		269 a.a.
269 a.a.
Protein chains
Pfam   ArchSchema ?
P07596  (IAAS_HORVU) -  Alpha-amylase/subtilisin inhibitor from Hordeum vulgare
Seq:
Struc: 		203 a.a.
181 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.3.4.21.62  - subtilisin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1. Hydrolyzes peptide amides.

 

 
DOI no: 10.1016/j.jmb.2008.05.034 J Mol Biol 380:681-690 (2008)
PubMed id: 18556023  
 
 
Structural and mutational analyses of the interaction between the barley alpha-amylase/subtilisin inhibitor and the subtilisin savinase reveal a novel mode of inhibition.
P.O.Micheelsen, J.Vévodová, L.De Maria, P.R.Ostergaard, E.P.Friis, K.Wilson, M.Skjøt.
 
  ABSTRACT  
 
Subtilisins represent a large class of microbial serine proteases. To date, there are three-dimensional structures of proteinaceous inhibitors from three families in complex with subtilisins in the Protein Data Bank. All interact with subtilisin via an exposed loop covering six interacting residues. Here we present the crystal structure of the complex between the Bacillus lentus subtilisin Savinase and the barley alpha-amylase/subtilisin inhibitor (BASI). This is the first reported structure of a cereal Kunitz-P family inhibitor in complex with a subtilisin. Structural analysis revealed that BASI inhibits Savinase in a novel way, as the interacting loop is shorter than loops previously reported. Mutational analysis showed that Thr88 is crucial for the inhibition, as it stabilises the interacting loop through intramolecular interactions with the BASI backbone.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Subtilisin inhibition modes. Upper panel: The subtilisin surface is shown in white, and residues in contact with the inhibitor are shown in blue. Residues of the inhibitor spanning subsites P4′ to P9 are shown as red sticks. Lower panel: Zoom-in on the interaction. P5–P2′ inhibitor residues and interacting subtilisin residues are shown as sticks; subtilisin residues, active site residues and inhibitor residues are shown in blue, yellow and red, respectively. β-Strands are shown as arrows. (a) BASI (this work, chains A and C). (b) SSI (2SIC). (c) CI-2 (2SNI). (d) OMTKY3 (1YU6, chains A and C). 		Figure 4.
Fig. 4. BASI plasticity II. The side chains of the interacting residues are shown as sticks; BASI residues are shown in red, and the surface of Savinase is shown in blue. (a) BASI–Savinase, corresponding to chains A and C. (b) BASI–Savinase, corresponding to chains B and D of this work.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 380, 681-690) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20535822 A.Sircar, S.Chaudhury, K.P.Kilambi, M.Berrondo, and J.J.Gray (2010).
A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19.
  Proteins, 78, 3115-3123.  
20602351 C.Pons, A.Solernou, L.Perez-Cano, S.Grosdidier, and J.Fernandez-Recio (2010).
Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding.
  Proteins, 78, 3182-3188.  
20607855 E.Mashiach, D.Schneidman-Duhovny, A.Peri, Y.Shavit, R.Nussinov, and H.J.Wolfson (2010).
An integrated suite of fast docking algorithms.
  Proteins, 78, 3197-3204.  
20936681 H.Hwang, T.Vreven, B.G.Pierce, J.H.Hung, and Z.Weng (2010).
Performance of ZDOCK and ZRANK in CAPRI rounds 13-19.
  Proteins, 78, 3104-3110.  
20589643 J.Janin (2010).
The targets of CAPRI Rounds 13-19.
  Proteins, 78, 3067-3072.  
20665475 M.Bueno, N.A.Temiz, and C.J.Camacho (2010).
Novel modulation factor quantifies the role of water molecules in protein interactions.
  Proteins, 78, 3226-3234.  
20607697 M.Eisenstein, A.Ben-Shimon, Z.Frankenstein, and N.Kowalsman (2010).
CAPRI targets T29-T42: proving ground for new docking procedures.
  Proteins, 78, 3174-3181.  
20806235 M.F.Lensink, and S.J.Wodak (2010).
Docking and scoring protein interactions: CAPRI 2009.
  Proteins, 78, 3073-3084.  
20839234 M.F.Lensink, and S.J.Wodak (2010).
Blind predictions of protein interfaces by docking calculations in CAPRI.
  Proteins, 78, 3085-3095.  
19846555 M.Renko, J.Sabotic, M.Mihelic, J.Brzin, J.Kos, and D.Turk (2010).
Versatile loops in mycocypins inhibit three protease families.
  J Biol Chem, 285, 308-316.
PDB codes: 3h6q 3h6r 3h6s
20715290 S.Fiorucci, and M.Zacharias (2010).
Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT.
  Proteins, 78, 3131-3139.  
20718048 S.J.de Vries, A.S.Melquiond, P.L.Kastritis, E.Karaca, A.Bordogna, M.van Dijk, J.P.Rodrigues, and A.M.Bonvin (2010).
Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions.
  Proteins, 78, 3242-3249.  
20528916 S.Kumar, N.Singh, M.Sinha, D.Dube, S.B.Singh, A.Bhushan, P.Kaur, A.Srinivasan, S.Sharma, and T.P.Singh (2010).
Crystal structure determination and inhibition studies of a novel xylanase and alpha-amylase inhibitor protein (XAIP) from Scadoxus multiflorus.
  FEBS J, 277, 2868-2882.
PDB codes: 3hu7 3m7s
20589642 S.Qin, and H.X.Zhou (2010).
Selection of near-native poses in CAPRI rounds 13-19.
  Proteins, 78, 3166-3173.  
20635420 S.Y.Huang, and X.Zou (2010).
MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19.
  Proteins, 78, 3096-3103.  
20552581 X.Li, I.H.Moal, and P.A.Bates (2010).
Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular crowding.
  Proteins, 78, 3189-3196.  
19452551 N.Kowalsman, and M.Eisenstein (2009).
Combining interface core and whole interface descriptors in postscan processing of protein-protein docking models.
  Proteins, 77, 297-318.  
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.

 

spacer
spacer