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(-) Description

Title :  CRYSTAL STRUCTURE OF BARLEY ALPHA-AMYLASE ISOZYME 1 (AMY1) INACTIVE MUTANT D180A IN COMPLEX WITH ACARBOSE
 
Authors :  X. Robert, R. Haser, N. Aghajari
Date :  03 Dec 03  (Deposition) - 07 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Amylase, Barley, Isozyme 1, Inactive Mutant, Beta- Alpha-Barrel, X-Ray Diffraction, Sugar Tongs Binding Site, Acarbose, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Robert, R. Haser, H. Mori, B. Svensson, N. Aghajari
Oligosaccharide Binding To Barley {Alpha}-Amylase 1
J. Biol. Chem. V. 280 32968 2005
PubMed-ID: 16030022  |  Reference-DOI: 10.1074/JBC.M505515200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-AMYLASE TYPE 1 ISOZYME
    Chains: A
    EC Number: 3.2.1.1
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPICZA
    Expression System Strain: GS115
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Gene: AMY1.1
    Mutation: YES
    Organism Scientific: HORDEUM VULGARE
    Organism Taxid: 4513
    Synonym: 1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE, AMY1, LOW PI ALPHA-AMYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA3Ligand/IonCALCIUM ION
3DAF3Ligand/Ion1,4-DEOXY-4-((5-HYDROXYMETHYL-2,3,4-TRIHYDROXYCYCLOHEX-5-ENYL)AMINO)FRUCTOSE
4GLC5Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:28 , ASP A:234 , TRP A:278 , TRP A:279 , HOH A:726 , HOH A:865 , HOH A:1558 , HOH A:1577 , BGC A:4001BINDING SITE FOR RESIDUE DAF A 4000
02AC2SOFTWAREGLN A:227 , VAL A:230 , TRP A:278 , HOH A:1346 , DAF A:4000 , GLC A:4002BINDING SITE FOR RESIDUE BGC A 4001
03AC3SOFTWAREGLN A:269 , LYS A:271 , HOH A:793 , BGC A:4001BINDING SITE FOR RESIDUE GLC A 4002
04AC4SOFTWAREVAL A:47 , MET A:53 , ALA A:146 , HOH A:1234 , GLC A:2001BINDING SITE FOR RESIDUE DAF A 2000
05AC5SOFTWARETRP A:10 , SER A:48 , TYR A:52 , MET A:53 , GLN A:296 , MET A:298 , HOH A:617 , HOH A:700 , HOH A:1315 , HOH A:1403 , DAF A:2000 , GLC A:2002BINDING SITE FOR RESIDUE GLC A 2001
06AC6SOFTWAREHIS A:93 , PHE A:144 , ARG A:178 , ALA A:180 , PHE A:181 , GLU A:205 , HIS A:290 , ASP A:291 , HOH A:1528 , HOH A:1531 , GLC A:2001BINDING SITE FOR RESIDUE GLC A 2002
07AC7SOFTWARELYS A:375 , TYR A:380 , ASP A:381 , VAL A:382 , GLY A:383 , HIS A:395 , GLY A:396 , ASP A:398 , TYR A:399 , TRP A:402 , GLC A:3001BINDING SITE FOR RESIDUE DAF A 3000
08AC8SOFTWARETYR A:380 , HIS A:395 , GLY A:396 , ASP A:398 , HOH A:904 , HOH A:1545 , DAF A:3000 , GLC A:3002BINDING SITE FOR RESIDUE GLC A 3001
09AC9SOFTWAREALA A:240 , TYR A:380 , HOH A:1545 , GLC A:3001BINDING SITE FOR RESIDUE GLC A 3002
10BC1SOFTWAREASN A:92 , ASP A:139 , ALA A:142 , ASP A:149 , GLY A:184 , HOH A:630BINDING SITE FOR RESIDUE CA A 500
11BC2SOFTWAREGLU A:109 , THR A:112 , ASP A:114 , ASP A:118 , HOH A:604 , HOH A:656BINDING SITE FOR RESIDUE CA A 501
12BC3SOFTWAREASP A:128 , ASP A:143 , PHE A:144 , ALA A:147 , ASP A:149 , HOH A:788BINDING SITE FOR RESIDUE CA A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RP9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RP9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RP9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RP9)

(-) Exons   (0, 0)

(no "Exon" information available for 1RP9)

(-) Sequences/Alignments

Asymmetric/Biological 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:404
 aligned with AMY1_HORVU | P00693 from UniProtKB/Swiss-Prot  Length:438

    Alignment length:404
                                    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    
           AMY1_HORVU    25 HQVLFQGFNWESWKQSGGWYNMMMGKVDDIAAAGVTHVWLPPPSHSVSNEGYMPGRLYDIDASKYGNAAELKSLIGALHGKGVQAIADIVINHRCADYKDSRGIYCIFEGGTSDGRLDWGPHMICRDDTKYSDGTANLDTGADFAAAPDIDHLNDRVQRELKEWLLWLKSDLGFDAWRLDFARGYSPEMAKVYIDGTSPSLAVAEVWDNMATGGDGKPNYDQDAHRQNLVNWVDKVGGAASAGMVFDFTTKGILNAAVEGELWRLIDPQGKAPGVMGWWPAKAATFVDNHDTGSTQAMWPFPSDKVMQGYAYILTHPGIPCIFYDHFFNWGFKDQIAALVAIRKRNGITATSALKILMHEGDAYVAEIDGKVVVKIGSRYDVGAVIPAGFVTSAHGNDYAVWEK 428
               SCOP domains d1rp9a2 A:1-347 Plant alpha-amylase                                                                                                                                                                                                                                                                                                                        d1rp9a1 A:348-404 Plant alpha-amylase                     SCOP domains
               CATH domains -1rp9A01 A:2-347 Glycosidases                                                                                                                                                                                                                                                                                                                              1rp9A02 A:348-404 Golgi alpha-mannosidase II              CATH domains
               Pfam domains -----------------Alpha-amylase-1rp9A01 A:18-326                                                                                                                                                                                                                                                                                       -----------------Alpha-amyl_C2-1rp9A02 A:344-404                               Pfam domains
         Sec.struct. author ...eee....hhhhh..hhhhhhhhhhhhhhhh...eeee..........................hhhhhhhhhhhhhhh..eeeeee........ee.....eee............hhhhh.............................hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhh...eee.................hhhhhhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhh..hhhhhh.......hhhhhhhh.eeee...............hhhhhhhhhhhhhhh..eeeeehhhhhh..hhhhhhhhhhhhhhh.......eeeeeee..eeeeee...eeeee..............eeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rp9 A   1 HQVLFQGFNWESWKQSGGWYNMMMGKVDDIAAAGVTHVWLPPPSHSVSNEGYMPGRLYDIDASKYGNAAELKSLIGALHGKGVQAIADIVINHRCADYKDSRGIYCIFEGGTSDGRLDWGPHMICRDDTKYSDGTANLDTGADFAAAPDIDHLNDRVQRELKEWLLWLKSDLGFDAWRLAFARGYSPEMAKVYIDGTSPSLAVAEVWDNMATGGDGKPNYDQDAHRQNLVNWVDKVGGAASAGMVFDFTTKGILNAAVEGELWRLIDPQGKAPGVMGWWPAKAVTFVDNHDTGSTQAMWPFPSDKVMQGYAYILTHPGIPCIFYDHFFNWGFKDQIAALVAIRKRNGITATSALKILMHEGDAYVAEIDGKVVVKIGSRYDVGAVIPAGFVTSAHGNDYAVWEK 404
                                    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
   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  (2, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)
(-)
Clan: no clan defined [family: Alpha-amyl_C2] (6)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMY1_HORVU | P00693)
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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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  1rp9
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 Related Entries

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

UniProtKB/Swiss-Prot
        AMY1_HORVU | P00693: 1ht6 1p6w 1rp8 1rpk 2qps 2qpu 3bsg 3bsh

(-) Related Entries Specified in the PDB File

1amy BARLEY ALPHA-AMYLASE ISOZYME 2 (AMY2) IN ITS NATIVE STATE
1bg9 BARLEY ALPHA-AMYLASE ISOZYME 2 (AMY2) IN COMPLEX WITH ACARBOSE
1ht6 BARLEY ALPHA-AMYLASE ISOZYME 1 (AMY1) IN ITS NATIVE STATE
1p6w BARLEY ALPHA-AMYLASE ISOZYME 1 (AMY1) IN COMPLEX WITH SUBSTRATE ANALOGUE METHYL 4I,4II,4III-TRI- THIOMALTOTETRAOSIDE (THIO-DP4)
1rp8 BARLEY ALPHA-AMYLASE ISOZYME 1 (AMY1) INACTIVE MUTANT D180A IN COMPLEX WITH MALTOHEPTAOSE
1rpk CRYSTAL STRUCTURE OF BARLEY ALPHA-AMYLASE ISOZYME 1 (AMY1) IN COMPLEX WITH ACARBOSE