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(-) Description

Title :  SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS
 
Authors :  A. Oubrie, H. J. Rozeboom, K. H. Kalk, J. A. Duine, B. W. Dijkstra
Date :  22 Apr 99  (Deposition) - 25 Feb 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Propeller, Superbarrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Oubrie, H. J. Rozeboom, K. H. Kalk, J. A. Duine, B. W. Dijkstra
The 1. 7 A Crystal Structure Of The Apo Form Of The Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus Reveals A Novel Internal Conserved Sequence Repeat.
J. Mol. Biol. V. 289 319 1999
PubMed-ID: 10366508  |  Reference-DOI: 10.1006/JMBI.1999.2766

(-) Compounds

Molecule 1 - SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE
    Cellular Location: PERIPLASM
    Chains: A, B
    EC Number: 1.1.99.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ACINETOBACTER CALCOACETICUS
    Organism Taxid: 471

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
3PT2Ligand/IonPLATINUM (II) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET B:400BINDING SITE FOR RESIDUE PT B 462
2AC2SOFTWAREGLU B:253 , TYR B:263 , HOH B:470 , HOH B:473 , HOH B:483 , HOH B:493BINDING SITE FOR RESIDUE CA B 463
3AC3SOFTWAREALA B:269 , TYR B:271 , ASP B:273 , GLU B:309 , HOH B:480 , HOH B:999BINDING SITE FOR RESIDUE CA B 464
4AC4SOFTWAREALA A:269 , TYR A:271 , ASP A:273 , GLU A:309 , HOH A:486 , HOH A:875BINDING SITE FOR RESIDUE CA A 465
5AC5SOFTWAREGLU A:253 , TYR A:263 , HOH A:487 , HOH A:500 , HOH A:504 , HOH A:521BINDING SITE FOR RESIDUE CA A 466
6AC6SOFTWAREGLY B:247 , PRO B:248 , HOH B:533 , HOH B:572 , HOH B:592BINDING SITE FOR RESIDUE CA B 467
7AC7SOFTWAREGLY A:247 , PRO A:248 , HOH A:520 , HOH A:664 , HOH A:672 , HOH A:870BINDING SITE FOR RESIDUE CA A 468
8AC8SOFTWAREGLN A:39 , ARG A:52 , ASN A:54 , SER A:59 , LYS A:61 , LEU B:23 , GLY B:58 , HOH B:816 , HOH B:1076BINDING SITE FOR RESIDUE GOL A 469

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Trp A:265 -Pro A:266
2Leu A:324 -Tyr A:325
3Trp B:265 -Pro B:266
4Leu B:324 -Tyr B:325

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QBI)

(-) 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:434
 aligned with DHGB_ACICA | P13650 from UniProtKB/Swiss-Prot  Length:478

    Alignment length:450
                                    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       434       444       454       464       474
           DHGB_ACICA    25 DVPLTPSQFAKAKSENFDKKVILSNLNKPHALLWGPDNQIWLTERATGKILRVNPESGSVKTVFQVPEIVNDADGQNGLLGFAFHPDFKNNPYIYISGTFKNPKSTDKELPNQTIIRRYTYNKSTDTLEKPVDLLAGLPSSKDHQSGRLVIGPDQKIYYTIGDQGRNQLAYLFLPNQAQHTPTQQELNGKDYHTYMGKVLRLNLDGSIPKDNPSFNGVVSHIYTLGHRNPQGLAFTPNGKLLQSEQGPNSDDEINLIVKGGNYGWPNVAGYKDDSGYAYANYSAAANKSIKDLAQNGVKVAAGVPVTKESEWTGKNFVPPLKTLYTVQDTYNYNDPTCGEMTYICWPTVAPSSAYVYKGGKKAITGWENTLLVPSLKRGVIFRIKLDPTYSTTYDDAVPMFKSNNRYRDVIASPDGNVLYVLTDTAGNVQKDDGSVTNTLENPGSLIKFT 474
               SCOP domains d1qbia_ A: Soluble quinoprotein glucose dehydrogenase                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1qbiA00 A:1-450 TolB, C-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhh......eeeeee.....eeeeee.....eeeee....eeeee......eeeeee.............eeeeee........eeeeeeeee...------.eeeeeeeeeee....eeeeeeeeeeee.......eeeeee.....eeeee......hhhhh..........hhhhhhh........eeeee...........ee..ee..eeee...eeeeeee.....eeeeee.....eeeeee.....................ee.hhhh....................eehhhhh.........eee..........----------..........ee.............eeeee......eeeeee......eeeeeeee......eeeeee......eeeee.....ee.....ee........eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qbi A   1 DVPLTPSQFAKAKSENFDKKVILSNLNKPHALLWGPDNQIWLTERATGKILRVNPESGSVKTVFQVPEIVNDADGQNGLLGFAFHPDFKNNPYIYISGTFKNPK------PNQTIIRRYTYNKSTDTLEKPVDLLAGLPSSKDHQSGRLVIGPDQKIYYTIGDQGRNQLAYLFLPNQAQHTPTQQELNGKDYHTYMGKVLRLNLDGSIPKDNPSFNGVVSHIYTLGHRNPQGLAFTPNGKLLQSEQGPNSDDEINLIVKGGNYGWPNVAGYKDDSGYAYANYSAAANKSIKDLAQNGVKVAAGVPVTKESEWTGKNFVPPLKTLYTVQDTYNYN----------CWPTVAPSSAYVYKGGKKAITGWENTLLVPSLKRGVIFRIKLDPTYSTTYDDAVPMFKSNNRYRDVIASPDGNVLYVLTDTAGNVQKDDGSVTNTLENPGSLIKFT 450
                                    10        20        30        40        50        60        70        80        90       100   |     -|      120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   |     -    |  350       360       370       380       390       400       410       420       430       440       450
                                                                                                                                 104    111                                                                                                                                                                                                                            334        345                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:436
 aligned with DHGB_ACICA | P13650 from UniProtKB/Swiss-Prot  Length:478

    Alignment length:452
                                    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       434       444       454       464       474  
           DHGB_ACICA    25 DVPLTPSQFAKAKSENFDKKVILSNLNKPHALLWGPDNQIWLTERATGKILRVNPESGSVKTVFQVPEIVNDADGQNGLLGFAFHPDFKNNPYIYISGTFKNPKSTDKELPNQTIIRRYTYNKSTDTLEKPVDLLAGLPSSKDHQSGRLVIGPDQKIYYTIGDQGRNQLAYLFLPNQAQHTPTQQELNGKDYHTYMGKVLRLNLDGSIPKDNPSFNGVVSHIYTLGHRNPQGLAFTPNGKLLQSEQGPNSDDEINLIVKGGNYGWPNVAGYKDDSGYAYANYSAAANKSIKDLAQNGVKVAAGVPVTKESEWTGKNFVPPLKTLYTVQDTYNYNDPTCGEMTYICWPTVAPSSAYVYKGGKKAITGWENTLLVPSLKRGVIFRIKLDPTYSTTYDDAVPMFKSNNRYRDVIASPDGNVLYVLTDTAGNVQKDDGSVTNTLENPGSLIKFTYK 476
               SCOP domains d1qbib_ B: Soluble quinoprotein glucose dehydrogenase                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1qbiB00 B:1-452 TolB, C-terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------      --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GSDH-1qbiB01           B:323-431                                                                             --------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------      --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GSDH-1qbiB02           B:323-431                                                                             --------------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------      --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GSDH-1qbiB03           B:323-431                                                                             --------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------      --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GSDH-1qbiB04           B:323-431                                                                             --------------------- Pfam domains (4)
         Sec.struct. author ....hhhhhhh.....eeeeeee.....eeeeee.....eeeee....eeeee......eeeeee.............eeeeee........eeeeeeeee...------.eeeeeeeeeee....eeeeeeeeeeee.......eeeeee.....eeeee......hhhhh..........hhhhhhh........eeeee...........ee..ee..eee....eeeeeee.....eeeeee.....eeeeee.....................ee.hhhh....................eehhhhh.........eee..........----------..........ee.............eeeee......eeeeee......eeeeeeee......eeeeee.....eeeeee.....ee.....ee........eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qbi B   1 DVPLTPSQFAKAKSENFDKKVILSNLNKPHALLWGPDNQIWLTERATGKILRVNPESGSVKTVFQVPEIVNDADGQNGLLGFAFHPDFKNNPYIYISGTFKNPK------PNQTIIRRYTYNKSTDTLEKPVDLLAGLPSSKDHQSGRLVIGPDQKIYYTIGDQGRNQLAYLFLPNQAQHTPTQQELNGKDYHTYMGKVLRLNLDGSIPKDNPSFNGVVSHIYTLGHRNPQGLAFTPNGKLLQSEQGPNSDDEINLIVKGGNYGWPNVAGYKDDSGYAYANYSAAANKSIKDLAQNGVKVAAGVPVTKESEWTGKNFVPPLKTLYTVQDTYNYN----------CWPTVAPSSAYVYKGGKKAITGWENTLLVPSLKRGVIFRIKLDPTYSTTYDDAVPMFKSNNRYRDVIASPDGNVLYVLTDTAGNVQKDDGSVTNTLENPGSLIKFTYK 452
                                    10        20        30        40        50        60        70        80        90       100   |     -|      120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   |     -    |  350       360       370       380       390       400       410       420       430       440       450  
                                                                                                                                 104    111                                                                                                                                                                                                                            334        345
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Beta_propeller (192)
(-)
Family: GSDH (5)
(-)
Acinetobacter calcoaceticus (1)
1aGSDH-1qbiB01B:323-431
1bGSDH-1qbiB02B:323-431
1cGSDH-1qbiB03B:323-431
1dGSDH-1qbiB04B:323-431

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DHGB_ACICA | P13650)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016901    oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
    GO:0048038    quinone binding    Interacting selectively and non-covalently with a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.
    GO:0008876    quinoprotein glucose dehydrogenase activity    Catalysis of the reaction: D-glucose + ubiquinone = D-glucono-1,5-lactone + ubiquinol.
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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DHGB_ACICA | P13650: 1c9u 1cq1 1cru

(-) Related Entries Specified in the PDB File

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