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(-) Description

Title :  AMY2/BASI PROTEIN-PROTEIN COMPLEX FROM BARLEY SEED
 
Authors :  F. Vallee, A. Kadziola, Y. Bourne, M. Juy, B. Svensson, R. Haser
Date :  15 Sep 97  (Deposition) - 16 Mar 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Hydrolase Inhibition, Enzyme Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Vallee, A. Kadziola, Y. Bourne, M. Juy, K. W. Rodenburg, B. Svensson, R. Haser
Barley Alpha-Amylase Bound To Its Endogenous Protein Inhibitor Basi: Crystal Structure Of The Complex At 1. 9 A Resolution.
Structure V. 6 649 1998
PubMed-ID: 9634702  |  Reference-DOI: 10.1016/S0969-2126(98)00066-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BARLEY ALPHA-AMYLASE 2(CV MENUET)
    Chains: A, B
    EC Number: 3.2.1.1
    Organ: SEED
    Organism Scientific: HORDEUM VULGARE
    Organism Taxid: 4513
    Synonym: AMY2
 
Molecule 2 - BARLEY ALPHA-AMYLASE/SUBTILISIN INHIBITOR
    Chains: C, D
    Organ: SEED
    Organism Scientific: HORDEUM VULGARE
    Organism Taxid: 4513
    Synonym: BASI

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:91 , ASP A:138 , ALA A:141 , ASP A:148 , GLY A:183 , HOH A:601BINDING SITE FOR RESIDUE CA A 500
02AC2SOFTWAREGLU A:108 , THR A:111 , ASP A:113 , ASP A:117 , HOH A:575BINDING SITE FOR RESIDUE CA A 501
03AC3SOFTWAREASP A:127 , ASP A:142 , PHE A:143 , ALA A:146 , ASP A:148 , HOH A:584BINDING SITE FOR RESIDUE CA A 502
04AC4SOFTWAREHOH A:597 , HOH A:611 , HOH A:612 , HOH A:644 , HOH A:741 , HOH A:795 , HOH C:185BINDING SITE FOR RESIDUE CA A 503
05AC5SOFTWAREASN B:91 , ASP B:138 , ALA B:141 , ASP B:148 , GLY B:183 , HOH B:582BINDING SITE FOR RESIDUE CA B 500
06AC6SOFTWAREGLU B:108 , THR B:111 , ASP B:113 , ASP B:117 , HOH B:664BINDING SITE FOR RESIDUE CA B 501
07AC7SOFTWAREASP B:127 , ASP B:142 , PHE B:143 , ALA B:146 , ASP B:148 , HOH B:581BINDING SITE FOR RESIDUE CA B 502
08AC8SOFTWAREHOH B:572 , HOH B:573 , HOH B:576 , HOH B:616 , HOH B:617 , HOH B:652 , HOH D:336BINDING SITE FOR RESIDUE CA B 503
09ACAUNKNOWNGLU A:204 , ASP A:289 , ASP A:179ACTIVE SITE.
10ACBUNKNOWNGLU B:204 , ASP B:289 , ASP B:179ACTIVE SITE.

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1C:43 -C:90
2C:144 -C:148
3D:43 -D:90
4D:144 -D:148

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Arg A:128 -Pro A:129
2Arg B:128 -Pro B:129
3Cys C:43 -Pro C:44
4Glu C:168 -Pro C:169
5Cys D:43 -Pro D:44
6Glu D:168 -Pro D:169

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AVA)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOYBEAN_KUNITZPS00283 Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.IAAS_HORVU28-44
 		  2C:6-22
D:6-22
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOYBEAN_KUNITZPS00283 Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.IAAS_HORVU28-44
 		  1C:6-22
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOYBEAN_KUNITZPS00283 Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.IAAS_HORVU28-44
 		  1-
D:6-22

(-) Exons   (0, 0)

(no "Exon" information available for 1AVA)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:403
 aligned with AMY2_HORVU | P04063 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:403
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424   
           AMY2_HORVU    25 QVLFQGFNWESWKHNGGWYNFLMGKVDDIAAAGITHVWLPPASQSVAEQGYMPGRLYDLDASKYGNKAQLKSLIGALHGKGVKAIADIVINHRTAEHKDGRGIYCIFEGGTPDARLDWGPHMICRDDRPYADGTGNPDTGADFGAAPDIDHLNLRVQKELVEWLNWLKADIGFDGWRFDFAKGYSADVAKIYIDRSEPSFAVAEIWTSLAYGGDGKPNLNQDQHRQELVNWVDKVGGKGPATTFDFTTKGILNVAVEGELWRLRGTDGKAPGMIGWWPAKAVTFVDNHDTGSTQHMWPFPSDRVMQGYAYILTHPGTPCIFYDHFFDWGLKEEIDRLVSVRTRHGIHNESKLQIIEADADLYLAEIDGKVIVKLGPRYDVGNLIPGGFKVAAHGNDYAVWEKI 427
               SCOP domains d1avaa2 A:1-346 Plant alpha-amylase                                                                                                                                                                                                                                                                                                                       d1avaa1 A:347-403 Plant alpha-amylase                     SCOP domains
               CATH domains 1avaA01 A:1-345 Glycosidases                                                                                                                                                                                                                                                                                                                             1avaA02 A:346-403 Golgi alpha-mannosidase II               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....hhh....hhhhhhhhhhhhhhh...eeee...........................hhhhhhhhhhhhhh..eeeeee.................................................................hhhhhhhhhhhhhhhh.....eeee..hhh..hhhhhhhhhhh...eeee..................hhhhhhhhhhhhhhh....eee..hhhhhhhhhh....hhhh.........hhhhhhhh.eee................hhhhhhhhhhhhh...eeeeehhhhh....hhhhhhhhhhhhh........eeeeeee..eeeeee...eeeee......hhh....eeeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ava A   1 QVLFQGFNWESWKHNGGWYNFLMGKVDDIAAAGITHVWLPPASQSVAEQGYMPGRLYDLDASKYGNKAQLKSLIGALHGKGVKAIADIVINHRTAEHKDGRGIYCIFEGGTPDARLDWGPHMICRDDRPYADGTGNPDTGADFGAAPDIDHLNLRVQKELVEWLNWLKADIGFDGWRFDFAKGYSADVAKIYIDRSEPSFAVAEIWTSLAYGGDGKPNLNQDQHRQELVNWVDKVGGKGPATTFDFTTKGILNVAVEGELWRLRGTDGKAPGMIGWWPAKAVTFVDNHDTGSTQHMWPFPSDRVMQGYAYILTHPGTPCIFYDHFFDWGLKEEIDRLVSVRTRHGIHNESKLQIIEADADLYLAEIDGKVIVKLGPRYDVGNLIPGGFKVAAHGNDYAVWEKI 403
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400   


Chain B from PDB  Type:PROTEIN  Length:403
 aligned with AMY2_HORVU | P04063 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:403
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424   
           AMY2_HORVU    25 QVLFQGFNWESWKHNGGWYNFLMGKVDDIAAAGITHVWLPPASQSVAEQGYMPGRLYDLDASKYGNKAQLKSLIGALHGKGVKAIADIVINHRTAEHKDGRGIYCIFEGGTPDARLDWGPHMICRDDRPYADGTGNPDTGADFGAAPDIDHLNLRVQKELVEWLNWLKADIGFDGWRFDFAKGYSADVAKIYIDRSEPSFAVAEIWTSLAYGGDGKPNLNQDQHRQELVNWVDKVGGKGPATTFDFTTKGILNVAVEGELWRLRGTDGKAPGMIGWWPAKAVTFVDNHDTGSTQHMWPFPSDRVMQGYAYILTHPGTPCIFYDHFFDWGLKEEIDRLVSVRTRHGIHNESKLQIIEADADLYLAEIDGKVIVKLGPRYDVGNLIPGGFKVAAHGNDYAVWEKI 427
               SCOP domains d1avab2 B:1-346 Plant alpha-amylase                                                                                                                                                                                                                                                                                                                       d1avab1 B:347-403 Plant alpha-amylase                     SCOP domains
               CATH domains 1avaB01 B:1-345 Glycosidases                                                                                                                                                                                                                                                                                                                             1avaB02 B:346-403 Golgi alpha-mannosidase II               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....hhh....hhhhhhh.hhhhhhh...eee............................hhhhhhhhhhhhhh..eeeeee...............................hhh...............................hhhhhhhhhhhhhhhh.....eeee..hhh..hhhhhhhhhhh...eeee..................hhhhhhhhhhhhhhh....eee..hhhhhhhhhh....hhhh.........hhhhhhhh.eee................hhhhhhhhhhhhh...eeeeehhhhh....hhhhhhhhhhhhh........eeeeeee..eeeeee...eeeee.............eeeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ava B   1 QVLFQGFNWESWKHNGGWYNFLMGKVDDIAAAGITHVWLPPASQSVAEQGYMPGRLYDLDASKYGNKAQLKSLIGALHGKGVKAIADIVINHRTAEHKDGRGIYCIFEGGTPDARLDWGPHMICRDDRPYADGTGNPDTGADFGAAPDIDHLNLRVQKELVEWLNWLKADIGFDGWRFDFAKGYSADVAKIYIDRSEPSFAVAEIWTSLAYGGDGKPNLNQDQHRQELVNWVDKVGGKGPATTFDFTTKGILNVAVEGELWRLRGTDGKAPGMIGWWPAKAVTFVDNHDTGSTQHMWPFPSDRVMQGYAYILTHPGTPCIFYDHFFDWGLKEEIDRLVSVRTRHGIHNESKLQIIEADADLYLAEIDGKVIVKLGPRYDVGNLIPGGFKVAAHGNDYAVWEKI 403
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400   


Chain C from PDB  Type:PROTEIN  Length:181
 aligned with IAAS_HORVU | P07596 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:181
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202 
           IAAS_HORVU    23 ADPPPVHDTDGHELRADANYYVLSANRAHGGGLTMAPGHGRHCPLFVSQDPNGQHDGFPVRITPYGVAPSDKIIRLSTDVRISFRAYTTCLQSTEWHIDSELAAGRRHVITGPVKDPSPSGRENAFRIEKYSGAEVHEYKLMSCGDWCQDLGVFRDLKGGAWFLGATEPYHVVVFKKAPPA 203
               SCOP domains d1avac_ C: Amylase/subtilisin inhibitor                                                                                                                                               SCOP domains
               CATH domains 1avaC00 C:1-181  [code=2.80.10.50, no name defined]                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeee..hhh...eeee.........eeee..........eeeee...............eeeee.....................................hhh.eeeee........eeeeee...eee.eee........eee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SOYBEAN_KUNITZ   --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ava C   1 ADPPPVHDTDGHELRADANYYVLSANRAHGGGLTMAPGHGRHCPLFVSQDPNGQHDGFPVRITPYGVAPSDKIIRLSTDVRISFRAYTTCLQSTEWHIDSELAAGRRHVITGPVKDPSPSGRENAFRIEKYSGAEVHEYKLMSCGDWCQDLGVFRDLKGGAWFLGATEPYHVVVFKKAPPA 181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 


Chain D from PDB  Type:PROTEIN  Length:181
 aligned with IAAS_HORVU | P07596 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:181
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202 
           IAAS_HORVU    23 ADPPPVHDTDGHELRADANYYVLSANRAHGGGLTMAPGHGRHCPLFVSQDPNGQHDGFPVRITPYGVAPSDKIIRLSTDVRISFRAYTTCLQSTEWHIDSELAAGRRHVITGPVKDPSPSGRENAFRIEKYSGAEVHEYKLMSCGDWCQDLGVFRDLKGGAWFLGATEPYHVVVFKKAPPA 203
               SCOP domains d1avad_ D: Amylase/subtilisin inhibitor                                                                                                                                               SCOP domains
               CATH domains 1avaD00 D:1-181  [code=2.80.10.50, no name defined]                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeee..hhh...eeee.........eeee..........eeeee...............eeeee.........................................eeeee........eeeeee...eee.eee...hhh..eee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SOYBEAN_KUNITZ   --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ava D   1 ADPPPVHDTDGHELRADANYYVLSANRAHGGGLTMAPGHGRHCPLFVSQDPNGQHDGFPVRITPYGVAPSDKIIRLSTDVRISFRAYTTCLQSTEWHIDSELAAGRRHVITGPVKDPSPSGRENAFRIEKYSGAEVHEYKLMSCGDWCQDLGVFRDLKGGAWFLGATEPYHVVVFKKAPPA 181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (3, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AVA)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (AMY2_HORVU | P04063)
molecular function
    GO:0004556    alpha-amylase activity    Catalysis of the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more alpha-(1->4)-linked D-glucose units.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0043169    cation binding    Interacting selectively and non-covalently with cations, charged atoms or groups of atoms with a net positive charge.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

Chain C,D   (IAAS_HORVU | P07596)
molecular function
    GO:0015066    alpha-amylase inhibitor activity    Stops, prevents or reduces the activity of alpha-amylase.
    GO:0004866    endopeptidase inhibitor activity    Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.

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  1ava
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  AMY2_HORVU | P04063
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  IAAS_HORVU | P07596
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        AMY2_HORVU | P04063: 1amy 1bg9
        IAAS_HORVU | P07596: 2iwt 3bx1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1AVA)