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PDBsum entry 1ava
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protein metals Protein-protein interface(s) links
Hydrolase inhibition PDB id
1ava

 

 

 

 

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Contents
Protein chains
403 a.a. *
181 a.a. *
Metals
_CA ×8
Waters ×748
* Residue conservation analysis
PDB id:
1ava
Name: Hydrolase inhibition
Title: Amy2/basi protein-protein complex from barley seed
Structure: Barley alpha-amylase 2(cv menuet). Chain: a, b. Synonym: amy2. Barley alpha-amylase/subtilisin inhibitor. Chain: c, d. Synonym: basi
Source: Hordeum vulgare. Organism_taxid: 4513. Organ: seed. Organ: seed
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.208     R-free:   0.269
Authors: F.Vallee,A.Kadziola,Y.Bourne,M.Juy,B.Svensson,R.Haser
Key ref:
F.Vallée et al. (1998). Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution. Structure, 6, 649-659. PubMed id: 9634702 DOI: 10.1016/S0969-2126(98)00066-5
Date:
15-Sep-97     Release date:   16-Mar-99    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04063  (AMY2_HORVU) -  Alpha-amylase type B isozyme from Hordeum vulgare
Seq:
Struc: 		427 a.a.
403 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.3.2.1.1  - alpha-amylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-alpha-glucosidic linkages in oligosaccharides and polysaccharides.

 

 
DOI no: 10.1016/S0969-2126(98)00066-5 Structure 6:649-659 (1998)
PubMed id: 9634702  
 
 
Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution.
F.Vallée, A.Kadziola, Y.Bourne, M.Juy, K.W.Rodenburg, B.Svensson, R.Haser.
 
  ABSTRACT  
 
BACKGROUND: Barley alpha-amylase is a 45 kDa enzyme which is involved in starch degradation during barley seed germination. The released sugars provide the plant embryo with energy for growth. The major barley alpha-amylase isozyme (AMY2) binds with high affinity to the endogenous inhibitor BASI (barley alpha-amylase/subtilisin inhibitor) whereas the minor isozyme (AMY1) is not inhibited. BASI is a 19.6 kDa bifunctional protein that can simultaneously inhibit AMY2 and serine proteases of the subtilisin family. This inhibitor may therefore prevent degradation of the endosperm starch during premature sprouting and protect the seed from attack by pathogens secreting proteases. RESULTS: The crystal structure of AMY2 in complex with BASI was determined and refined at 1.9 A resolution. BASI consists of a 12-stranded beta-barrel structure which belongs to the beta-trefoil fold family and inhibits AMY2 by sterically occluding access of the substrate to the active site of the enzyme. The AMY2-BASI complex is characterized by an unusual completely solvated calcium ion located at the protein-protein interface. CONCLUSIONS: The AMY2-BASI complex represents the first reported structure of an endogenous protein-protein complex from a higher plant. The structure of the complex throws light on the strict specificity of BASI for AMY2, and shows that domain B of AMY2 contributes greatly to the specificity of enzyme-inhibitor recognition. In contrast to the three-dimensional structures of porcine pancreatic alpha-amylase in complex with proteinaceous inhibitors, the AMY2-BASI structure reveals that the catalytically essential amino acid residues of the enzyme are not directly bound to the inhibitor. Binding of BASI to AMY2 creates a cavity, exposed to the external medium, that is ideally shaped to accommodate an extra calcium ion. This feature may contribute to the inhibitory effect, as the key amino acid sidechains of the active site are in direct contact with water molecules which are in turn ligated to the calcium ion.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Sequence comparison of AMY1 and AMY2 relevant to the interface area of the AMY2-BASI complex. Residues involved in the interaction with BASI are indicated by yellow rectangles. Calcium ligands are marked by pink, orange and blue circles for Ca500, Ca501 and Ca502, respectively. Non-conservative substitutions are indicated with red squares. Bold and underlined residues designate sidechain substitutions between AMY1 and AMY2 for residues in interaction with BASI. Domain B is outlined in green, whereas domain A is shaded in blue.
 
  The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 649-659) copyright 1998.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20931223 J.M.Mondego, M.P.Duarte, E.Kiyota, L.Martínez, S.R.de Camargo, F.P.De Caroli, B.S.Alves, S.M.Guerreiro, M.L.Oliva, O.Guerreiro-Filho, and M.Menossi (2011).
Molecular characterization of a miraculin-like gene differentially expressed during coffee development and coffee leaf miner infestation.
  Planta, 233, 123-137.  
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.  
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.  
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.  
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
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.  
19640842 R.Bao, C.Z.Zhou, C.Jiang, S.X.Lin, C.W.Chi, and Y.Chen (2009).
The ternary structure of the double-headed arrowhead protease inhibitor API-A complexed with two trypsins reveals a novel reactive site conformation.
  J Biol Chem, 284, 26676-26684.
PDB code: 3e8l
17444520 K.F.Lin, T.R.Lee, P.H.Tsai, M.P.Hsu, C.S.Chen, and P.C.Lyu (2007).
Structure-based protein engineering for alpha-amylase inhibitory activity of plant defensin.
  Proteins, 68, 530-540.
PDB code: 2gl1
17437525 K.S.Bak-Jensen, S.Laugesen, O.Ostergaard, C.Finnie, P.Roepstorff, and B.Svensson (2007).
Spatio-temporal profiling and degradation of alpha-amylase isozymes during barley seed germination.
  FEBS J, 274, 2552-2565.  
  17277441 N.Kulahin, V.Kiselyov, A.Kochoyan, O.Kristensen, J.S.Kastrup, V.Berezin, E.Bock, and M.Gajhede (2007).
Structure of rat acidic fibroblast growth factor at 1.4 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 65-68.
PDB code: 2j3p
17013936 R.Buckow, U.Weiss, V.Heinz, and D.Knorr (2007).
Stability and catalytic activity of alpha-amylase from barley malt at different pressure-temperature conditions.
  Biotechnol Bioeng, 97, 1.  
17803687 S.Bozonnet, M.T.Jensen, M.M.Nielsen, N.Aghajari, M.H.Jensen, B.Kramhøft, M.Willemoës, S.Tranier, R.Haser, and B.Svensson (2007).
The 'pair of sugar tongs' site on the non-catalytic domain C of barley alpha-amylase participates in substrate binding and activity.
  FEBS J, 274, 5055-5067.
PDB codes: 2qps 2qpu
17098195 K.Maeda, P.Hägglund, C.Finnie, B.Svensson, and A.Henriksen (2006).
Structural basis for target protein recognition by the protein disulfide reductase thioredoxin.
  Structure, 14, 1701-1710.
PDB code: 2iwt
  17142906 M.Azarkan, A.Garcia-Pino, R.Dibiani, L.Wyns, R.Loris, and D.Baeyens-Volant (2006).
Crystallization and preliminary X-ray analysis of a protease inhibitor from the latex of Carica papaya.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1239-1242.  
16717423 T.Yamasaki, M.Deguchi, T.Fujimoto, T.Masumura, T.Uno, K.Kanamaru, and H.Yamagata (2006).
Rice bifunctional alpha-amylase/subtilisin inhibitor: cloning and characterization of the recombinant inhibitor expressed in Escherichia coli.
  Biosci Biotechnol Biochem, 70, 1200-1209.  
  16880545 Y.H.Lin, W.Y.Peng, Y.C.Huang, H.H.Guan, Y.C.Hsieh, M.Y.Liu, T.Chang, and C.J.Chen (2006).
Purification, crystallization and preliminary X-ray crystallographic analysis of rice bifunctional alpha-amylase/subtilisin inhibitor from Oryza sativa.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 743-745.  
15657043 B.C.Bønsager, P.K.Nielsen, M.Abou Hachem, K.Fukuda, M.Praetorius-Ibba, and B.Svensson (2005).
Mutational analysis of target enzyme recognition of the beta-trefoil fold barley alpha-amylase/subtilisin inhibitor.
  J Biol Chem, 280, 14855-14864.  
15765494 K.Maeda, C.Finnie, and B.Svensson (2005).
Identification of thioredoxin h-reducible disulphides in proteomes by differential labelling of cysteines: insight into recognition and regulation of proteins in barley seeds by thioredoxin h.
  Proteomics, 5, 1634-1644.  
16356852 L.Dolecková-Maresová, M.Pavlík, M.Horn, and M.Mares (2005).
De novo design of alpha-amylase inhibitor: a small linear mimetic of macromolecular proteinaceous ligands.
  Chem Biol, 12, 1349-1357.  
16356842 N.Pohl (2005).
Acyclic peptide inhibitors of amylases.
  Chem Biol, 12, 1257-1258.  
12482867 A.Linden, O.Mayans, W.Meyer-Klaucke, G.Antranikian, and M.Wilmanns (2003).
Differential regulation of a hyperthermophilic alpha-amylase with a novel (Ca,Zn) two-metal center by zinc.
  J Biol Chem, 278, 9875-9884.
PDB codes: 1mwo 1mxd 1mxg
14627732 S.R.Brych, J.Kim, T.M.Logan, and M.Blaber (2003).
Accommodation of a highly symmetric core within a symmetric protein superfold.
  Protein Sci, 12, 2704-2718.
PDB codes: 1jy0 1m16 1nzk 1p63
12906828 X.Robert, R.Haser, T.E.Gottschalk, F.Ratajczak, H.Driguez, B.Svensson, and N.Aghajari (2003).
The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs.
  Structure, 11, 973-984.
PDB codes: 1ht6 1p6w
11856298 O.L.Franco, D.J.Rigden, F.R.Melo, and M.F.Grossi-De-Sá (2002).
Plant alpha-amylase inhibitors and their interaction with insect alpha-amylases.
  Eur J Biochem, 269, 397-412.  
12360523 O.L.Franco, M.F.Grossi de Sá, M.P.Sales, L.V.Mello, A.S.Oliveira, and D.J.Rigden (2002).
Overlapping binding sites for trypsin and papain on a Kunitz-type proteinase inhibitor from Prosopis juliflora.
  Proteins, 49, 335-341.  
11914496 X.Robert, T.E.Gottschalk, R.Haser, B.Svensson, and N.Aghajari (2002).
Expression, purification and preliminary crystallographic studies of alpha-amylase isozyme 1 from barley seeds.
  Acta Crystallogr D Biol Crystallogr, 58, 683-686.  
11284678 N.Alam, S.Gourinath, S.Dey, A.Srinivasan, and T.P.Singh (2001).
Substrate-inhibitor interactions in the kinetics of alpha-amylase inhibition by ragi alpha-amylase/trypsin inhibitor (RATI) and its various N-terminal fragments.
  Biochemistry, 40, 4229-4233.  
11025543 J.Lehtiö, T.T.Teeri, and P.A.Nygren (2000).
Alpha-amylase inhibitors selected from a combinatorial library of a cellulose binding domain scaffold.
  Proteins, 41, 316-322.  
10672010 K.W.Rodenburg, F.Vallée, N.Juge, N.Aghajari, X.Guo, R.Haser, and B.Svensson (2000).
Specific inhibition of barley alpha-amylase 2 by barley alpha-amylase/subtilisin inhibitor depends on charge interactions and can be conferred to isozyme 1 by mutation.
  Eur J Biochem, 267, 1019-1029.  
10713515 S.Gourinath, N.Alam, A.Srinivasan, C.Betzel, and T.P.Singh (2000).
Structure of the bifunctional inhibitor of trypsin and alpha-amylase from ragi seeds at 2.2 A resolution.
  Acta Crystallogr D Biol Crystallogr, 56, 287-293.
PDB code: 1b1u
10547530 G.André, A.Buléon, R.Haser, and V.Tran (1999).
Amylose chain behavior in an interacting context. III. Complete occupancy of the AMY2 barley alpha-amylase cleft and comparison with biochemical data.
  Biopolymers, 50, 751-762.  
10508777 P.J.Pereira, V.Lozanov, A.Patthy, R.Huber, W.Bode, S.Pongor, and S.Strobl (1999).
Specific inhibition of insect alpha-amylases: yellow meal worm alpha-amylase in complex with the amaranth alpha-amylase inhibitor at 2.0 A resolution.
  Structure, 7, 1079-1088.
PDB code: 1clv
9687373 S.Strobl, K.Maskos, G.Wiegand, R.Huber, F.X.Gomis-Rüth, and R.Glockshuber (1998).
A novel strategy for inhibition of alpha-amylases: yellow meal worm alpha-amylase in complex with the Ragi bifunctional inhibitor at 2.5 A resolution.
  Structure, 6, 911-921.
PDB code: 1tmq
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.

 

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