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(-) Description

Title :  CRYSTAL STRUCTURE OF QUINONE-DEPENDENT ALCOHOL DEHYDROGENASE FROM PSEUDOGLUCONOBACTER SACCHAROKETOGENENES WITH ZINC IN THE ACTIVE SITE
 
Authors :  H. J. Rozeboom, S. Yu, R. Mikkelsen, I. Nikolaev, H. Mulder, B. W. Dijkst
Date :  25 Mar 14  (Deposition) - 25 Mar 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Oxidoreductase, Carbohydrate Oxidation, Quinoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Rozeboom, S. Yu, R. Mikkelsen, I. Nikolaev, H. J. Mulder, B. W. Dijkstra
Crystal Structure Of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenes. A Versatile Dehydrogenase Oxidizing Alcohols And Carbohydrates.
Protein Sci. V. 24 2044 2015
PubMed-ID: 26440996  |  Reference-DOI: 10.1002/PRO.2818

(-) Compounds

Molecule 1 - ALCOHOL DEHYDROGENASE
    Chains: A
    EC Number: 1.1.2.8
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Common: PICHIA PASTORIS
    Expression System Plasmid: PPIC2-ADH
    Expression System Strain: GS115
    Expression System Taxid: 644223
    Fragment: RESIDUES 37-608
    Organism Scientific: PSEUDOGLUCONOBACTER SACCHAROKETOGENES
    Organism Taxid: 133921
    Strain: IFO 14464
    Synonym: QUINONE-DEPENDENT ALCOHOL DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric Unit (5, 11)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3PPI1Ligand/IonPROPANOIC ACID
4PQQ1Ligand/IonPYRROLOQUINOLINE QUINONE
5ZN7Ligand/IonZINC ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3PPI1Ligand/IonPROPANOIC ACID
4PQQ1Ligand/IonPYRROLOQUINOLINE QUINONE
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
3PPI2Ligand/IonPROPANOIC ACID
4PQQ2Ligand/IonPYRROLOQUINOLINE QUINONE
5ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:333 , PHE A:434 , TYR A:476 , PQQ A:1608BINDING SITE FOR RESIDUE PEG A1607
02AC2SOFTWAREGLU A:106 , LEU A:153 , ARG A:158 , SER A:203 , THR A:218 , GLN A:220 , TRP A:270 , ASP A:333 , GLU A:335 , LYS A:378 , PHE A:434 , LEU A:435 , ASP A:439 , TRP A:440 , TYR A:515 , PEG A:1607 , ZN A:1612 , HOH A:2118 , HOH A:2185 , HOH A:2260 , HOH A:2330BINDING SITE FOR RESIDUE PQQ A1608
03AC3SOFTWAREHIS A:324 , PPI A:1617 , HOH A:2369 , HOH A:2370 , HOH A:2374BINDING SITE FOR RESIDUE ZN A1609
04AC4SOFTWAREGLU A:300 , ASP A:350 , GLU A:503 , HOH A:2394 , HOH A:2499BINDING SITE FOR RESIDUE ZN A1610
05AC5SOFTWAREASP A:57 , GLU A:262 , CL A:1616 , HOH A:2010BINDING SITE FOR RESIDUE ZN A1611
06AC6SOFTWAREGLN A:220 , ASP A:333 , GLU A:335 , PQQ A:1608BINDING SITE FOR RESIDUE ZN A1612
07AC7SOFTWAREGLU A:545 , SER A:548 , HOH A:2522 , HOH A:2523 , HOH A:2529BINDING SITE FOR RESIDUE ZN A1613
08AC8SOFTWAREASP A:276 , GLU A:278 , LYS A:370 , ZN A:1615BINDING SITE FOR RESIDUE ZN A1614
09AC9SOFTWAREZN A:1614 , HOH A:2337 , HOH A:2569BINDING SITE FOR RESIDUE ZN A1615
10BC1SOFTWAREASP A:57 , ASN A:62 , ASN A:65 , ASN A:113 , ZN A:1611BINDING SITE FOR RESIDUE CL A1616
11BC2SOFTWAREHIS A:324 , THR A:410 , ZN A:1609 , HOH A:2369 , HOH A:2370 , HOH A:2374 , HOH A:2439BINDING SITE FOR RESIDUE PPI A1617

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:219 -A:226
2A:336 -A:377
3A:431 -A:460

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:290 -Pro A:291
2Cys A:431 -Pro A:432
3Gly A:436 -Gly A:437

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CVC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CVC)

(-) Exons   (0, 0)

(no "Exon" information available for 4CVC)

(-) Sequences/Alignments

Asymmetric 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:562
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh..................ee........hhhhheeeeeee.........eeee..eeeee....eeeeee.....eeeeee....hhhhh.hhhhhh....eee..eeeee....eeeeee.....eeeeee...hhhhh.......eee..eeee...........eeeeee.....eeeeee........hhhhh...hhhhh.........eee....eeeee.......hhhhhh..........eeeee......eeeeee...............eeeeee.........eeee........eeeeeee.......eeeee.....eeeee.......eeee.....eee.hhhh.......eee.............eee....eeeeeee.eeeeeee.....hhhhh..eeeeeee.......eeeeeee.....eeeeeee.......eeee...eeeee....eeeeee.....eeeeee........eeeeee..eeeeeeee...hhhhhhhhhh..........eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cvc A  45 SAIENFQPVTADDLAGKNPANWPILRGNYQGWGYSPLDQINKDNVGDLQLVWSRTMEPGSNEGAAIAYNGVIFLGNTNDVIQAIDGKTGSLIWEYRRKLPSASKFINSLGAAKRSIALFGDKVYFVSWDNFVVALDAKTGKLAWETNRGQGVEEGVANSSGPIVVDGVVIAGSTCQFSGFGCYVTGTDAESGEELWRNTFIPRPGEEGDDTWGGAPYENRWMTGAWGQITYDPELDLVYYGSTGAGPASEVQRGTEGGTLAGTNTRFAVKPKTGEVVWKHQTLPRDNWDSECTFEMMVVSTSVNPDAKADGMMSVGANVPRGETRKVLTGVPCKTGVAWQFDAKTGDYFWSKATVEQNSIASIDDTGLVTVNEDMILKEPGKTYNYCPTFLGGRDWPSAGYLPKSNLYVIPLSNACYDVMARTTEATPADVYNTDATLVLAPGKTNMGRVDAIDLATGETKWSYETRAALYDPVLTTGGDLVFVGGIDRDFRALDAESGKEVWSTRLPGAVSGYTTSYSIDGRQYVAVVSGGSLGGPTFGPTTPDVDSASGANGIYVFALPE 606
                                    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       484       494       504       514       524       534       544       554       564       574       584       594       604
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4CVC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CVC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CVC)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)

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4cvb CRYSTAL STRUCTURE OF QUINONE-DEPENDENT ALCOHOL DEHYDROGENASE FORM PSEUDOGLUCONOBACTER SACCHAROKETOGENENES