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(-) Description

Title :  CRYSTAL STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 ALPHA-AMYLASE 1 (TVAI) MUTANT D356N COMPLEXED WITH P2, A PULLULAN MODEL OLIGOSACCHARIDE
 
Authors :  A. Abe, H. Yoshida, T. Tonozuka, Y. Sakano, S. Kamitori
Date :  02 Aug 05  (Deposition) - 11 Jul 06  (Release) - 04 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Amylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Abe, H. Yoshida, T. Tonozuka, Y. Sakano, S. Kamitori
Complexes Of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 And Pullulan Model Oligossacharides Provide New Insight Into The Mechanism For Recognizing Substrates With Alpha-(1, 6) Glycosidic Linkages
Febs J. V. 272 6145 2005
PubMed-ID: 16302977  |  Reference-DOI: 10.1111/J.1742-4658.2005.05013.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-AMYLASE I
    Chains: A
    EC Number: 3.2.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: THERMOACTINOMYCES VULGARIS
    Organism Taxid: 2026
    Strain: R-47
    Synonym: TVA I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2CA3Ligand/IonCALCIUM ION
3GLC6Ligand/IonALPHA-D-GLUCOSE
4MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:546 , GLN A:547 , PRO A:549 , GLC A:702 , HOH A:2444BINDING SITE FOR RESIDUE GLC A 701
02AC2SOFTWAREASP A:180 , SER A:182 , GLC A:701 , GLC A:703 , HOH A:2126 , HOH A:2147BINDING SITE FOR RESIDUE GLC A 702
03AC3SOFTWARESER A:182 , THR A:219 , HIS A:221 , SER A:315 , GLC A:702 , GLC A:704 , HOH A:2085 , HOH A:2248 , HOH A:2404BINDING SITE FOR RESIDUE GLC A 703
04AC4SOFTWAREHIS A:221 , TYR A:223 , ASP A:516 , ARG A:520 , GLC A:703 , BGC A:705 , HOH A:2404 , HOH A:2437BINDING SITE FOR RESIDUE GLC A 704
05AC5SOFTWARETYR A:223 , HIS A:267 , PHE A:310 , ASN A:356 , GLU A:396 , HIS A:471 , ASP A:472 , GLC A:704 , HOH A:2010BINDING SITE FOR RESIDUE BGC A 705
06AC6SOFTWAREASN A:3 , GLC A:802 , HOH A:2097BINDING SITE FOR RESIDUE GLC A 801
07AC7SOFTWAREGLY A:41 , ILE A:43 , TRP A:65 , ASP A:75 , GLC A:801 , BGC A:803BINDING SITE FOR RESIDUE GLC A 802
08AC8SOFTWARELYS A:40 , TRP A:65 , ASN A:68 , ASP A:75 , GLC A:802BINDING SITE FOR RESIDUE BGC A 803
09AC9SOFTWAREALA A:2 , ASP A:4 , ASN A:6 , ASP A:42 , ASP A:96 , HOH A:2019BINDING SITE FOR RESIDUE CA A 2001
10BC1SOFTWAREASN A:145 , ASP A:147 , ASN A:150 , ASP A:151 , GLY A:187 , ASP A:189 , HOH A:2037BINDING SITE FOR RESIDUE CA A 2002
11BC2SOFTWAREASP A:276 , ASN A:279 , PHE A:281 , SER A:283 , GLU A:288 , HOH A:2013BINDING SITE FOR RESIDUE CA A 2003
12BC3SOFTWAREASN A:10 , LEU A:12 , MET A:557 , THR A:558 , LEU A:559 , GLN A:598 , HOH A:2255BINDING SITE FOR RESIDUE MPD A 1001
13BC4SOFTWAREGLY A:170 , SER A:171 , SER A:533 , ALA A:536 , LEU A:537 , LYS A:540 , TYR A:631BINDING SITE FOR RESIDUE MPD A 1002
14BC5SOFTWARETHR A:73 , PRO A:347 , TRP A:597 , ASN A:620BINDING SITE FOR RESIDUE MPD A 1003
15BC6SOFTWAREGLU A:165 , TRP A:485 , SER A:587 , GLY A:629 , HOH A:2442BINDING SITE FOR RESIDUE MPD A 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D0F)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Trp A:303 -Pro A:304
2Pro A:346 -Pro A:347
3Asp A:516 -Pro A:517

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D0F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D0F)

(-) Exons   (0, 0)

(no "Exon" information available for 2D0F)

(-) 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:637
 aligned with NEPU1_THEVU | Q60053 from UniProtKB/Swiss-Prot  Length:666

    Alignment length:637
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       
          NEPU1_THEVU    30 AANDNNVEWNGLFHDQGPLFDNAPEPTSTQSVTLKLRTFKGDITSANIKYWDTADNAFHWVPMVWDSNDPTGTFDYWKGTIPASPSIKYYRFQINDGTSTAWYNGNGPSSTEPNADDFYIIPNFKTPDWLKNGVMYQIFPDRFYNGDSSNDVQTGSYTYNGTPTEKKAWGSSVYADPGYDNSLVFFGGDLAGIDQKLGYIKKTLGANILYLNPIFKAPTNHKYDTQDYMAVDPAFGDNSTLQTLINDIHSTANGPKGYLILDGVFNHTGDSHPWFDKYNNFSSQGAYESQSSPWYNYYTFYTWPDSYASFLGFNSLPKLNYGNSGSAVRGVIYNNSNSVAKTYLNPPYSVDGWRLDAAQYVDANGNNGSDVTNHQIWSEFRNAVKGVNSNAAIIGEYWGNANPWTAQGNQWDAATNFDGFTQPVSEWITGKDYQNNSASISTTQFDSWLRGTRANYPTNVQQSMMNFLSNHDITRFATRSGGDLWKTYLALIFQMTYVGTPTIYYGDEYGMQGGADPDNRRSFDWSQATPSNSAVALTQKLITIRNQYPALRTGSFMTLITDDTNKIYSYGRFDNVNRIAVVLNNDSVSHTVNVPVWQLSMPNGSTVTDKITGHSYTVQNGMVTVAVDGHYGAVLAQ 666
               SCOP domains d2d0fa1 A:1-122 automated matches                                                                                         d2d0fa3 A:123-554 automated matches                                                                                                                                                                                                                                                                                                                                                                                                             d2d0fa2 A:555-637 automated matches                                                 SCOP domains
               CATH domains 2d0fA01 A:1-124 Immunoglobulins                                                                                             2d0fA02 A:125-547 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                         2d0fA03 A:548-637 Golgi alpha-mannosidase II                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh...................eeeeeeee.....eeeeeeee....eeeeee.eeeee.....eeeeeeee......eeeeeeeee..eeeeee..eee........eee......hhhhhhh.eeeehhhhh...hhhhh......ee..ee.ee.............hhh.ee...hhhhhhhhhhhhhh.....eeee...ee..........eeeee.....hhhhhhhhhhhhhh.......eeeeee..............................hhhhh.eee...ee.ee..eeeee........hhhhhhhh....hhhhhhhh......eeee..............hhhhhhhhhhhhhhhhhhh...eeee.....hhhhh.......ee.....hhhhhhhhhh...........hhhhhhhhhhhhhh..hhhhhhhheee.......hhhhhh..hhhhhhhhhhhhh....eeeee.hhhhh.............hhhhh...hhhhhhhhhhhhhhhhhhhhhhheeeeeeee....eeeeeee....eeeeeee.....eeeeehhhhhh.....eeee.....eee.....eeeee...eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d0f A   1 AANDNNVEWNGLFHDQGPLFDNAPEPTSTQSVTLKLRTFKGDITSANIKYWDTADNAFHWVPMVWDSNDPTGTFDYWKGTIPASPSIKYYRFQINDGTSTAWYNGNGPSSTEPNADDFYIIPNFKTPDWLKNGVMYQIFPDRFYNGDSSNDVQTGSYTYNGTPTEKKAWGSSVYADPGYDNSLVFFGGDLAGIDQKLGYIKKTLGANILYLNPIFKAPTNHKYDTQDYMAVDPAFGDNSTLQTLINDIHSTANGPKGYLILDGVFNHTGDSHPWFDKYNNFSSQGAYESQSSPWYNYYTFYTWPDSYASFLGFNSLPKLNYGNSGSAVRGVIYNNSNSVAKTYLNPPYSVDGWRLNAAQYVDANGNNGSDVTNHQIWSEFRNAVKGVNSNAAIIGEYWGNANPWTAQGNQWDAATNFDGFTQPVSEWITGKDYQNNSASISTTQFDSWLRGTRANYPTNVQQSMMNFLSNHDITRFATRSGGDLWKTYLALIFQMTYVGTPTIYYGDEYGMQGGADPDNRRSFDWSQATPSNSAVALTQKLITIRNQYPALRTGSFMTLITDDTNKIYSYGRFDNVNRIAVVLNNDSVSHTVNVPVWQLSMPNGSTVTDKITGHSYTVQNGMVTVAVDGHYGAVLAQ 637
                                    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       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630
   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, 3)

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

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D0F)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NEPU1_THEVU | Q60053)
molecular function
    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:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0031216    neopullulanase activity    Catalysis of the hydrolysis of pullulan to panose (6-alpha-D-glucosylmaltose).
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.

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  2d0f
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 Related Entries

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

UniProtKB/Swiss-Prot
        NEPU1_THEVU | Q60053: 1izj 1izk 1ji1 1uh2 1uh3 1uh4 2d0g 2d0h

(-) Related Entries Specified in the PDB File

1ji1 CRYSTAL STRUCTURE ANALYSIS OF THERMOACTINOMYCES VULGARIS R- 47 ALPHA-AMYLASE 1
2d0g THE SAME PROTEIN, D356N/E396Q MUTANT COMPLEXED WITH P5, A PULLULAN MODEL OLIGOSACCHARIDE
2d0h THE SAME PROTEIN, D356N/E396Q MUTANT COMPLEXED WITH P2, A PULLULAN MODEL OLIGOSACCHARIDE