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(-) Description

Title :  STRUCTURE OF AN ALPHA-AMYLASE FROM MALBRANCHEA CINNAMOMEA
 
Authors :  P. Zhou, S. Q. Hu, Y. Zhou, P. Han, S. Q. Yang, Z. Q. Jiang
Date :  09 Dec 11  (Deposition) - 29 May 13  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Malbranchea Cinnamomea C -Amylase Cmodels, Protein Conformation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Han, P. Zhou, S. Hu, S. Yang, Q. Yan, Z. Q. Jiang
A Novel Multifunctional Alpha-Amylase From The Thermophilic Fungus Malbranchea Cinnamomea: Biochemical Characterization And Three-Dimensional Structure.
Appl Biochem Biotechnol. V. 170 420 2013
PubMed-ID: 23536251  |  Reference-DOI: 10.1007/S12010-013-0198-Y

(-) Compounds

Molecule 1 - ALPHA-AMYLASE
    Chains: A
    Organism Scientific: MALBRANCHEA CINNAMOMEA
    Organism Taxid: 5041

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GLC1Ligand/IonALPHA-D-GLUCOSE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:141 , GLU A:181 , ASP A:194 , HIS A:229 , HOH A:612 , HOH A:648 , HOH A:680BINDING SITE FOR RESIDUE CA A 501
2AC2SOFTWARESER A:155 , ASN A:161 , HOH A:941BINDING SITE FOR RESIDUE NAG A 502
3AC3SOFTWAREASP A:225 , THR A:226 , HIS A:229 , GLU A:249 , TYR A:251 , ASP A:316 , HOH A:610 , HOH A:756 , HOH A:758BINDING SITE FOR RESIDUE GLC A 503
4AC4SOFTWAREASN A:239 , ASP A:240 , TRP A:264 , VAL A:265 , ASP A:266BINDING SITE FOR RESIDUE TRS A 504

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:51 -A:59
2A:170 -A:183
3A:259 -A:302
4A:455 -A:490

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asn A:158 -Pro A:159
2Ala A:189 -Asn A:190
3Asp A:359 -Pro A:360

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VM7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VM7)

(-) Exons   (0, 0)

(no "Exon" information available for 3VM7)

(-) 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:470
 aligned with K9L8F3_MALCI | K9L8F3 from UniProtKB/TrEMBL  Length:492

    Alignment length:470
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491
         K9L8F3_MALCI    22 ATPDEWRSRSIYQVLTDRFARGDGSPDAPCDTGARKYCGGNYRGLISQLDYIQGMGFDSVWISPITKQFEDDWNGAPYHGYWQTDLYALNEHFGTEEDLRALADELHARGMFLMVDVVINHNGWPGDAASIDYSQFNPFNSSDYYHPPCEINYDDQTSVEQCWLYTGANALPDLKTEDPHVSQVHNDWIADLVSKYSIDGLRIDTTKHVDKPAIGSFNDAAGVYAVGEVYHGDPAYTCPYQDWVDGVLNFPVYYPLIDAFKSPSGTMWSLVDNINKVFQTCNDPRLLGTFSENHDIPRFASYTQDLALAKNVLAFTILFDGIPIVYAGQEQQYSGDSDPYNREALWLSGFNTDAPLYKHIAACNRIRSHAVSNDDAYITTPTDIKYSDDHTLALVKGAVTTVLTNAGANAGETTVTVEATGYASGEQVTDVLSCESIAASDGGRLSVTLNQGLPRVFFPTDALAGSGLCE 491
               SCOP domains d3vm7a1 A:22-400 automated matches                                                                                                                                                                                                                                                                                                                                                         d3vm7a2 A:401-491 automated matches                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...eee.hhhhhh..........hhhhh.....hhhhhhhhhhhhhhh...eeee...eee..............eeeeeee.....hhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhh....hhhhh.........hhhhhhhh...............hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhh..ee.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhh.eee.......hhhhhh.hhhhhhhhhhhhhhh..eeeee.hhhhh...........hhhhhh....hhhhhhhhhhhhhhhhhhhhh........eeeee...eeeeee..eeeeee.......eeeeee.........eeee....eeee.hhhhheeeeee....eeeee.hhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vm7 A  22 ATPDEWRSRSIYQVLTDRFARGDGSPDAPCDTGARKYCGGNYRGLISQLDYIQGMGFDSVWISPITKQFEDDWNGAPYHGYWQTDLYALNEHFGTEEDLRALADELHARGMFLMVDVVINHNGWPGDAASIDYSQFNPFNSSDYYHPPCEINYDDQTSVEQCWLYTGANALPDLKTEDPHVSQVHNDWIADLVSKYSIDGLRIDTTKHVDKPAIGSFNDAAGVYAVGEVYHGDPAYTCPYQDWVDGVLNFPVYYPLIDAFKSPSGTMWSLVDNINKVFQTCNDPRLLGTFSENHDIPRFASYTQDLALAKNVLAFTILFDGIPIVYAGQEQQYSGDSDPYNREALWLSGFNTDAPLYKHIAACNRIRSHAVSNDDAYITTPTDIKYSDDHTLALVKGAVTTVLTNAGANAGETTVTVEATGYASGEQVTDVLSCESIAASDGGRLSVTLNQGLPRVFFPTDALAGSGLCE 491
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491
   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  (0, 0)

(no "CATH Domain" information available for 3VM7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VM7)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (K9L8F3_MALCI | K9L8F3)
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: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:0016052    carbohydrate catabolic process    The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
    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.

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