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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUCODEXTRANASE FROM ARTHROBACTER GLOBIFORMIS I42
 
Authors :  M. Mizuno, T. Tonozuka, S. Suzuki, R. Uotsu-Tomita, A. Ohtaki, S. Kamit A. Nishikawa, Y. Sakano
Date :  16 Jun 03  (Deposition) - 09 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Alpha-Six-Barrels, Gh Family 15, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Mizuno, T. Tonozuka, S. Suzuki, R. Uotsu-Tomita, S. Kamitori, A. Nishikawa, Y. Sakano
Structural Insights Into Substrate Specificity And Function Of Glucodextranase
J. Biol. Chem. V. 279 10575 2004
PubMed-ID: 14660574  |  Reference-DOI: 10.1074/JBC.M310771200

(-) Compounds

Molecule 1 - GLUCODEXTRANASE
    ChainsA
    EC Number3.2.1.70
    Organism ScientificARTHROBACTER GLOBIFORMIS
    Organism Taxid1665
    StrainI42

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:139 , THR A:142 , GLY A:144 , ASP A:146 , ASP A:159BINDING SITE FOR RESIDUE CA A 2001
2AC2SOFTWAREPHE A:358 , GLN A:362 , GLU A:409 , HOH A:3404BINDING SITE FOR RESIDUE CA A 2002
3AC3SOFTWAREASP A:136 , PRO A:137 , ASN A:211 , ILE A:212 , HOH A:3061BINDING SITE FOR RESIDUE CA A 2003
4AC4SOFTWAREVAL A:946 , ALA A:969 , ASP A:980 , ASP A:982 , ASP A:985BINDING SITE FOR RESIDUE CA A 2004
5AC5SOFTWAREASP A:782 , PRO A:783 , ASP A:786 , ASP A:807 , LEU A:808 , ASP A:990BINDING SITE FOR RESIDUE CA A 2005
6AC6SOFTWAREASP A:782 , ASP A:786 , ASP A:990 , VAL A:991 , GLN A:999 , HOH A:3199BINDING SITE FOR RESIDUE CA A 2006
7AC7SOFTWAREGLY A:526 , LEU A:529 , TRP A:565 , LEU A:594 , GLU A:597 , ARG A:598 , HOH A:3163BINDING SITE FOR RESIDUE GOL A 3001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UG9)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Ser A:8 -Pro A:9
2Tyr A:47 -Pro A:48
3Gly A:208 -Pro A:209
4Ser A:651 -Pro A:652
5Ala A:698 -Pro A:699
6Asp A:956 -Pro A:957
7Ser A:1009 -Pro A:1010

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UG9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UG9)

(-) Exons   (0, 0)

(no "Exon" information available for 1UG9)

(-) 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:1019
 aligned with Q9LBQ9_ARTGO | Q9LBQ9 from UniProtKB/TrEMBL  Length:1048

    Alignment length:1019
                                    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       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      1039         
        Q9LBQ9_ARTGO     30 TAEPPGSPGAAATWTKGDKEGVGTSLNPASKVWYTLTEGTMSEVYYPHADTPNTRELQFAVSDGTSAQRESEQTTRTVELADPKALSYRQTTTDNAGRWRLTKTYVTDPRRSTVMLGVTFEVLDGGDYQLFVLSDPSLAGTSGGDTGSVTDGALLASDLADAATPVATALVSSVGFGAVANGYVGTSDGWTDLAADGRLDNASATAGPGNISQTGQIPLAAGGKTEFSLALGFGADTAEALATAKASLGTGYKKVSKSYTGEWKKYLNSLDAPATSLTGALRTQYDVSLMTVKSHEDKTFPGAFIASLTIPWGQAASAETHREGYHAVWARDMYQSVTALLAAGDEEAAARGVEWLFTYQQQPDGHFPQTSRVDGTIGQNGIQLDETAFPILLANQIGRTDAGFYRNELKPAADYLVAAGPKTPQERWEETGGYSTSTLASQIAALAAAADIAGKNGDAGSAAVYRATADEWQRSTEKWMFTTNGPVGDGKYYLRISATGNPNDGATRDWGNGAGVHPENAVLDGGFLEFVRLGVKAPADPYVADSLAETDASISQETPGGRMWHRYTYDGYGEKADGSPWDGTGIGRLWPLLSGERGEYALANGQDALPYLETMHSAANAGYMIPEQVWDRDEPTSYGHELGRSTGSASPLSWAMAQYVRLAAGVKAGAPVETPQNVAARYAAGTPLSSPELSVTAPEALSTADSATAVVRGTTNAAKVYVSVNGTATEAPVTDGTFSLDVALTGAKNKVTVAAVAADGGTAVEDRTVLYYGSRIGALSDPAGDDNGPGTYRYPTNSAYVPGAFDLTGVDVYDAGDDYAFVATIAGEVTNPWGGQAISHQRVNIYLGKGEGGATPGLPGTNINLEHAWDSVIVTDGRFDGAGVYAPDGTRTSAVSLLAVPEARQIVTRVPKAALGGLDPATARMSVAMFGNAESGEGIGNVRPVYDGAYWEAGDPAWIKEWRFGGGAGVFDGTIPSRDTDTDDPNALDVLVGEGQTQAAVLDWRAGSPVVVPMLGLQP 1048
               SCOP domains d1ug9a4 A:2-273 Glucodextranase, domain N                                                                                                                                                                                                                                       d1ug9a1 A:274-686 Glucodextranase, domain A                                                                                                                                                                                                                                                                                                                                                                                  d1ug9a2 A:687-775 Glucodextranase, domain B                                              d1ug9a3 A:776-1020 Glucodextranase, domain C                                                                                                                                                                                                          SCOP domains
               CATH domains 1ug9A01 A:2-273  [code=2.70.98.10, no name defined]                                                                                                                                                                                                                             1ug9A02 A:274-687  [code=1.50.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                                         1ug9A03 A:688-773 E-set domains of sugar-utilizing enzymes; domain 3                  1ug9A04 A:774-938,A:939-1020  [code=2.60.40.1190, no name defined]                                                                                                   1ug9A04 A:774-938,A:939-1020  [code=2.60.40.1190, no name defined]                 CATH domains
           Pfam domains (1) ---Glucodextran_N-1ug9A04 A:5-271                                                                                                                                                                                                                                             ---------Glyco_hydro_15-1ug9A01 A:281-956                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    ---------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Glucodextran_B-1ug9A03 A:692-775                                                    DUF2223-1ug9A02 A:776-1018                                                                                                                                                                                                                         -- Pfam domains (2)
         Sec.struct. author ....................eee.........eeeee..eeeeee........eeeeeeeee....eee.hhh.eeeeee.......eeeeee.....eeeeeeeee.....eeeeeeeeee......eeeeeeee.hhhh...eeeeee..eeeeee.......eeeeeee.....eeeeee....hhhhhhhhhh.......eeeee.eeeeeee......eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh................hhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.............eehhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhee.........ee..ee.........eee......eee.hhh.hhhhhhhhhh......hhhhhhhhhhhhhhheeee..eeee..........................hhhhhhhhhhhhhh...hhhhhhhhhhh.................................hhhhhhhhhhhhhhhhhh.....hhhhhhhhh.........eeeee...eee....eeeeeeee...eeeeee..eeeee.....eeeeeee....eeeeeeeee.....eeeeeeeee...eeeeeee..........................eeeeeeeee..eeeeeeee...............eeeeeeee......ee.hhhh.eee.....eeeeee......eee.....eee..eeeeehhh.eeeeeee.hhh........eeeeeeee..hhhhh......eeehhhhhhh.hhhhhhhheeee.....................ee......hhhhhhhhhhh..eee..ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ug9 A    2 TAEPPGSPGAAATWTKGDKEGVGTSLNPASKVWYTLTEGTMSEVYYPHADTPNTRELQFAVSDGTSAQRESEQTTRTVELADPKALSYRQTTTDNAGRWRLTKTYVTDPRRSTVMLGVTFEVLDGGDYQLFVLSDPSLAGTSGGDTGSVTDGALLASDLADAATPVATALVSSVGFGAVANGYVGTSDGWTDLAADGRLDNASATAGPGNISQTGQIPLAAGGKTEFSLALGFGADTAEALATAKASLGTGYKKVSKSYTGEWKKYLNSLDAPATSLTGALRTQYDVSLMTVKSHEDKTFPGAFIASLTIPWGQAASAETHREGYHAVWARDMYQSVTALLAAGDEEAAARGVEWLFTYQQQPDGHFPQTSRVDGTIGQNGIQLDETAFPILLANQIGRTDAGFYRNELKPAADYLVAAGPKTPQERWEETGGYSTSTLASQIAALAAAADIAGKNGDAGSAAVYRATADEWQRSTEKWMFTTNGPVGDGKYYLRISATGNPNDGATRDWGNGAGVHPENAVLDGGFLEFVRLGVKAPADPYVADSLAETDASISQETPGGRMWHRYTYDGYGEKADGSPWDGTGIGRLWPLLSGERGEYALANGQDALPYLETMHSAANAGYMIPEQVWDRDEPTSYGHELGRSTGSASPLSWAMAQYVRLAAGVKAGAPVETPQNVAARYAAGTPLSSPELSVTAPEALSTADSATAVVRGTTNAAKVYVSVNGTATEAPVTDGTFSLDVALTGAKNKVTVAAVAADGGTAVEDRTVLYYGSRIGALSDPAGDDNGPGTYRYPTNSAYVPGAFDLTGVDVYDAGDDYAFVATIAGEVTNPWGGQAISHQRVNIYLGKGEGGATPGLPGTNINLEHAWDSVIVTDGRFDGAGVYAPDGTRTSAVSLLAVPEARQIVTRVPKAALGGLDPATARMSVAMFGNAESGEGIGNVRPVYDGAYWEAGDPAWIKEWRFGGGAGVFDGTIPSRDTDTDDPNALDVLVGEGQTQAAVLDWRAGSPVVVPMLGLQP 1020
                                    11        21        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       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011         

   Legend:   → Mismatch (orange background)
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    → 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  (4, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (4, 4)

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

(-) Pfam Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Clan: 6_Hairpin (120)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9LBQ9_ARTGO | Q9LBQ9)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    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:0004339    glucan 1,4-alpha-glucosidase activity    Catalysis of the hydrolysis of terminal (1->4)-linked alpha-D-glucose residues successively from non-reducing ends of the chains with release of beta-D-glucose.
    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.
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:0005976    polysaccharide metabolic process    The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9LBQ9_ARTGO | Q9LBQ91ulv

(-) Related Entries Specified in the PDB File

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