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(-) Description

Title :  THERMOACTINOMYCES VULGARIS R-47 ALPHA-AMYLASE 1/MALTO-TRIDECAOSE COMPLEX
 
Authors :  A. Abe, T. Tonozuka, Y. Sakano, S. Kamitori
Date :  24 Jun 03  (Deposition) - 13 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Starch Binding Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Abe, T. Tonozuka, Y. Sakano, S. Kamitori
Complex Structures Of Thermoactinomyces Vulgaris R-47 Alpha-Amylase 1 With Malto-Oligosaccharides Demonstrate The Role Of Domain N Acting As A Starch-Binding Domain
J. Mol. Biol. V. 335 811 2004
PubMed-ID: 14687576  |  Reference-DOI: 10.1016/J.JMB.2003.10.078
(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 Plasmid: PUC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: THERMOACTINOMYCES VULGARIS
    Organism Taxid: 2026
    Strain: R-47
    Synonym: ALPHA-AMYLASE, TVA I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric/Biological Unit (4, 22)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2CA3Ligand/IonCALCIUM ION
3GLC16Ligand/IonALPHA-D-GLUCOSE
4MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:182 , PHE A:313 , ASP A:516 , GLC A:702BINDING SITE FOR RESIDUE GLC A 701
02AC2SOFTWAREHIS A:221 , TYR A:223 , ASP A:516 , ARG A:520 , GLC A:701 , GLC A:703 , HOH A:2131 , HOH A:2231 , HOH A:2240BINDING SITE FOR RESIDUE GLC A 702
03AC3SOFTWARETYR A:223 , HIS A:267 , PHE A:310 , ARG A:354 , ASN A:356 , ALA A:357 , GLN A:396 , HIS A:471 , ASP A:472 , GLC A:702 , HOH A:2391BINDING SITE FOR RESIDUE GLC A 703
04AC4SOFTWAREASN A:402 , PRO A:403 , GLC A:802 , HOH A:2578 , HOH A:2589BINDING SITE FOR RESIDUE GLC A 801
05AC5SOFTWARETYR A:89 , ALA A:115 , ASP A:116 , ASP A:117 , TYR A:119 , ASN A:402 , ALA A:406 , GLC A:801 , GLC A:803 , HOH A:2045 , HOH A:2076BINDING SITE FOR RESIDUE GLC A 802
06AC6SOFTWARETRP A:51 , TYR A:89 , ARG A:91 , ASP A:117 , GLC A:802 , GLC A:804 , HOH A:2612 , HOH A:2651BINDING SITE FOR RESIDUE GLC A 803
07AC7SOFTWAREPHE A:58 , ARG A:91 , ASN A:114 , GLC A:803 , GLC A:805 , HOH A:2190BINDING SITE FOR RESIDUE GLC A 804
08AC8SOFTWAREGLC A:804BINDING SITE FOR RESIDUE GLC A 805
09AC9SOFTWARETRP A:448 , BGC A:811 , HOH A:2256 , HOH A:2700BINDING SITE FOR RESIDUE BGC A 810
10BC1SOFTWAREASP A:418 , TRP A:448 , BGC A:810 , GLC A:812 , HOH A:2508BINDING SITE FOR RESIDUE BGC A 811
11BC2SOFTWAREASN A:400 , ASP A:418 , ASN A:455 , BGC A:811 , HOH A:2368BINDING SITE FOR RESIDUE GLC A 812
12BC3SOFTWAREGLC A:902BINDING SITE FOR RESIDUE GLC A 901
13BC4SOFTWAREGLC A:901 , GLC A:903BINDING SITE FOR RESIDUE GLC A 902
14BC5SOFTWAREASN A:3 , ILE A:43 , THR A:44 , GLC A:902 , GLC A:904 , HOH A:2354 , HOH A:2367 , HOH A:2605BINDING SITE FOR RESIDUE GLC A 903
15BC6SOFTWAREGLY A:41 , ILE A:43 , TRP A:65 , ASP A:75 , GLC A:903 , GLC A:905 , HOH A:2075 , HOH A:2109 , HOH A:2685BINDING SITE FOR RESIDUE GLC A 904
16BC7SOFTWARELYS A:40 , TRP A:65 , ASN A:68 , ASP A:75 , GLC A:904 , GLC A:906 , HOH A:2581BINDING SITE FOR RESIDUE GLC A 905
17BC8SOFTWAREGLC A:905 , HOH A:2528BINDING SITE FOR RESIDUE GLC A 906
18BC9SOFTWAREGLN A:153 , THR A:154 , TRP A:485 , ASP A:628 , GLY A:629BINDING SITE FOR RESIDUE GLC A 910
19CC1SOFTWAREALA A:2 , ASP A:4 , ASN A:6 , ASP A:42 , ASP A:96 , HOH A:2232BINDING SITE FOR RESIDUE CA A 1001
20CC2SOFTWAREASN A:145 , ASP A:147 , ASN A:150 , ASP A:151 , GLY A:187 , ASP A:189 , HOH A:2067BINDING SITE FOR RESIDUE CA A 1002
21CC3SOFTWAREASP A:276 , ASN A:279 , PHE A:281 , SER A:283 , GLU A:288 , HOH A:2749BINDING SITE FOR RESIDUE CA A 1003
22CC4SOFTWAREASP A:446 , THR A:558 , LEU A:559 , HOH A:2649BINDING SITE FOR RESIDUE MPD A 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UH4)

(-) 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 1UH4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UH4)

(-) Exons   (0, 0)

(no "Exon" information available for 1UH4)

(-) 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 d1uh4a1 A:1-122 Maltogenic amylase, N-terminal domain N                                                                   d1uh4a3 A:123-554 Maltogenic amylase, central domain                                                                                                                                                                                                                                                                                                                                                                                            d1uh4a2 A:555-637 Maltogenic amylase                                                SCOP domains
               CATH domains 1uh4A01 A:1-124 Immunoglobulins                                                                                             1uh4A02 A:125-547 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                         1uh4A03 A:548-637 Golgi alpha-mannosidase II                                               CATH domains
               Pfam domains ----------Alpha-amylase_N-1uh4A02 A:11-125                                                                                   --------------------------------------------------------------Alpha-amylase-1uh4A01 A:188-517                                                                                                                                                                                                                                                                                                           ------------------------------------------------------------------------------------------------------------------------ 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..hhhhhh..eee.......hhhhhh..hhhhhhhhhhhhh....eeeee.hhhhh.....................hhhhhhhhhhhhhhhhhhhhhhheeeeeeee....eeeeeee....eeeeeee.....eeeeehhhhhh.....eeee.....eee.....eeeee...eeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uh4 A   1 AANDNNVEWNGLFHDQGPLFDNAPEPTSTQSVTLKLRTFKGDITSANIKYWDTADNAFHWVPMVWDSNDPTGTFDYWKGTIPASPSIKYYRFQINDGTSTAWYNGNGPSSTEPNADDFYIIPNFKTPDWLKNGVMYQIFPDRFYNGDSSNDVQTGSYTYNGTPTEKKAWGSSVYADPGYDNSLVFFGGDLAGIDQKLGYIKKTLGANILYLNPIFKAPTNHKYDTQDYMAVDPAFGDNSTLQTLINDIHSTANGPKGYLILDGVFNHTGDSHPWFDKYNNFSSQGAYESQSSPWYNYYTFYTWPDSYASFLGFNSLPKLNYGNSGSAVRGVIYNNSNSVAKTYLNPPYSVDGWRLNAAQYVDANGNNGSDVTNHQIWSEFRNAVKGVNSNAAIIGQYWGNANPWTAQGNQWDAATNFDGFTQPVSEWITGKDYQNNSASISTTQFDSWLRGTRANYPTNVQQSMMNFLSNHDITRFATRSGGDLWKTYLALIFQMTYVGTPTIYYGDEYGMQGGADPDNRRSFDWSQATPSNSAVALTQKLITIRNQYPALRTGSFMTLITDDTNKIYSYGRFDNVNRIAVVLNNDSVSHTVNVPVWQLSMPNGSTVTDKITGHSYTVQNGMVTVAVDGHYGAVLAQ 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  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)
(-)
Clan: no clan defined [family: Alpha-amylase_N] (16)

(-) 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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  1uh4
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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 2d0f 2d0g 2d0h

(-) Related Entries Specified in the PDB File

1ji1 STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 ALPHA-AMYLASE 1
1uh2 STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 ALPHA-AMYLASE 1/MALTO-HEXAOSE COMPLEX
1uh3 STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 ALPHA-AMYLASE 1/ACARBOSE COMPLEX