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(-) Description

Title :  ACTIVE SITE METAL DEPLETED ALDOS-2-ULOSE DEHYDRATASE
 
Authors :  M. Claesson, Y. Lindqvist, S. Madrid, T. Sandalova, R. Fiskesund, S. Yu G. Schneider
Date :  15 Nov 11  (Deposition) - 21 Mar 12  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Lyase, Dehydratase/Isomerase, Lignin Degradation, Cortalcerone/Microthecin Forming, Metalloenzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Claesson, Y. Lindqvist, S. Madrid, T. Sandalova, R. Fiskesund, S. Yu, G. Schneider
Crystal Structure Of Bifunctional Aldos-2-Ulose Dehydratase/Isomerase From Phanerochaete Chrysosporium With The Reaction Intermediate Ascopyrone M.
J. Mol. Biol. V. 417 279 2012
PubMed-ID: 22330145  |  Reference-DOI: 10.1016/J.JMB.2012.02.001

(-) Compounds

Molecule 1 - ALDOS-2-ULOSE DEHYDRATASE
    Chains: A
    EC Number: 4.2.1.110
    Engineered: YES
    Expression System: OGATAEA ANGUSTA
    Expression System Strain: RB11(URA-)
    Expression System Taxid: 870730
    Expression System Vector: PFPMT121
    Organism Common: WHITE ROT FUNGUS
    Organism Scientific: PHANEROCHAETE CHRYSOSPORIUM
    Organism Taxid: 5306
    Synonym: D-ARABINO-HEX-2-ULOSE DEHYDRATASE, PYRANOSONE DEHYDRATASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2NHF2Ligand/Ion1,5-ANHYDRO-D-FRUCTOSE
3ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NHF4Ligand/Ion1,5-ANHYDRO-D-FRUCTOSE
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:343 , ASP A:345 , ASP A:347 , GLU A:349 , GLU A:351BINDING SITE FOR RESIDUE ZN A 951
2AC2SOFTWAREASP A:101 , THR A:103 , ASN A:105 , PHE A:107 , ASP A:109BINDING SITE FOR RESIDUE MG A 952
3AC3SOFTWAREPHE A:595 , TRP A:619 , ALA A:627 , HIS A:630 , HIS A:632 , GLU A:639 , HIS A:641 , TRP A:726BINDING SITE FOR RESIDUE NHF A 953
4AC4SOFTWAREARG A:450 , ALA A:494 , PHE A:605 , VAL A:612 , HOH A:2043BINDING SITE FOR RESIDUE NHF A 954

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A7Y)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Glu A:292 -Ala A:293
2Asp A:360 -Pro A:361
3Pro A:548 -Pro A:549
4Ile A:599 -Gly A:600
5Ser A:719 -Pro A:720
6Thr A:739 -Pro A:740
7Trp A:818 -Pro A:819

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A7Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A7Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4A7Y)

(-) 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:880
 aligned with AUD_PHACH | P84193 from UniProtKB/Swiss-Prot  Length:900

    Alignment length:886
                                    24        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       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894      
            AUD_PHACH    15 QPAALPLFQPQLVQGGRPDGYWVEAFPFRSDSSKCPNIIGYGLGTYDMKSDIQMLVNPYATTNNQSSSWTPVPLAKLDFPVAMHYADITKNGFNDVIITDQYGSSMDDIWAYGGRVSWLENPGELRDNWTMRTIGHSPGMHRLKAGHFTRTDRVQVVAVPIVVASSDLTTPADVIIFTAPDDPRSEQLWQRDVVGTRHLVHEVAIVPAAETDGEMRFDQIILAGRDGVDCLWYDGARWQRHLVGTGLPEERGDPYWGAGSAAVGRVGDDYAGYICSAEAFHGNTVSVYTKPAGSPTGIVRAEWTRHVLDVFGPLNGKHTGSIHQVVCADIDGDGEDEFLVAMMGADPPDFQRTGVWCYKLVDRTNMKFSKTKVSSVSAGRIATANFHSQGSEVDIATISYSVPGYFESPNPSINVFLSTGILAERLDEEVMLRVVRAGSTRFKTEMEFLDVAGKKLTLVVLPPFARLDVERNVSGVKVMAGTVCWADENGKHERVPATRPFGCESMIVSADYLESGEEGAILVLYKPSSTSGRPPFRSMDELVAHNLFPAYVPDSVRAMKFPWVRCADRPWAHGRFKDLDFFNLIGFHVNFADDSAAVLAHVQLWTAGIGVSAGFHNHVEASFCEIHACIANGTGRGGMRWATVPDANFNPDSPNLEDTELIVVPDMHEHGPLWRTRPDGHPLLRMNDTIDYPWHAWLAGAGNPSPQAFDVWVAFEFPGFETFSTPPPPRVLEPGRYAIRFGDPHQTASLALQKNDATDGTPVLALLDLDGGPSPQAWNISHVPGTDMYEIAHAKTGSLVCARWPPVKNQRVAGTHSPAAMGLTSRWAVTKNTKGQITFRLPEAPDHGPLFLSVSAIRHQQEADAIPVIVQGDSIELSAWSLVPAN 900
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee.......eeeee..........eeeee........eeeeee.hhhhh.........eeeeeee.....eeee........eeeeee..eee..ee.....eeeee...........eeeeee...eeeeeee........eeeeee...........eeeeeee...........eeeeeeee....eeeeehhhhhh......eeeeee..eeeeeee....eeeeeee...............eeeeeee..eeeeeeeeee.....eeeeee..............eeeeeee...........eeeeeee........eeeeeee.....hhh.eeeeeeeeee....eeeeeeee.....eeeee.........eeeee..ee...ee.....eeeeeee.eeeee....eeeee.hhhhh...eeeeeeee..eeeeeeee....eee......eeeeeeeeeeeee..eeeee........eee......eeeeeeeeeeeeeeee...........hhhhh.ee......hhhhhh.....ee.hhh...........eeeeeeeeeee......eeeeeeeeee................eeeeeeee......eeeee..hhhhh.....hhh.eeeee....eee........................eeee...........eeeeeeee.................eeeeeeee...........hhh..............................................................hhhhh....eeee.....eeee..........eeee...------.eeeeeee...hhhhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a7y A  15 QPAALPLFQPQLVQGGRPDGYWVEAFPFRSDSSKCPNIIGYGLGTYDMKSDIQMLVNPYATTNNQSSSWTPVPLAKLDFPVAMHYADITKNGFNDVIITDQYGSSMDDIWAYGGRVSWLENPGELRDNWTMRTIGHSPGMHRLKAGHFTRTDRVQVVAVPIVVASSDLTTPADVIIFTAPDDPRSEQLWQRDVVGTRHLVHEVAIVPAAETDGEMRFDQIILAGRDGVDCLWYDGARWQRHLVGTGLPEERGDPYWGAGSAAVGRVGDDYAGYICSAEAFHGNTVSVYTKPAGSPTGIVRAEWTRHVLDVFGPLNGKHTGSIHQVVCADIDGDGEDEFLVAMMGADPPDFQRTGVWCYKLVDRTNMKFSKTKVSSVSAGRIATANFHSQGSEVDIATISYSVPGYFESPNPSINVFLSTGILAERLDEEVMLRVVRAGSTRFKTEMEFLDVAGKKLTLVVLPPFARLDVERNVSGVKVMAGTVCWADENGKHERVPATRPFGCESMIVSADYLESGEEGAILVLYKPSSTSGRPPFRSMDELVAHNLFPAYVPDSVRAMKFPWVRCADRPWAHGRFKDLDFFNLIGFHVNFADDSAAVLAHVQLWTAGIGVSAGFHNHVEASFCEIHACIANGTGRGGMRWATVPDANFNPDSPNLEDTELIVVPDMHEHGPLWRTRPDGHPLLRMNDTIDYPWHAWLAGAGNPSPQAFDVWVAFEFPGFETFSTPPPPRVLEPGRYAIRFGDPHQTASLALQKNDATDGTPVLALLDLDGGPSPQAWNISHVPGTDMYEIAHAKTGSLVCARWPPVKNQRVAGTHSPAAMGLTSRWAVTKNTKGQITFRLPEAPDHGPLFLSVSAI------DAIPVIVQGDSIELSAWSLVPAN 900
                                    24        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       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864      |  -   |   884       894      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  871    878
   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  (0, 0)

(no "SCOP Domain" information available for 4A7Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A7Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A7Y)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (AUD_PHACH | P84193)
molecular function
    GO:0033991    aldos-2-ulose dehydratase activity    Catalysis of the reactions: 1,5-anhydro-D-fructose = 2-hydroxy-2-(hydroxymethyl)-2H-pyran-3(6H)-one + H2O; (1a) 1,5-anhydro-D-fructose = 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose + H2O and (1b) 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose = 2-hydroxy-2-(hydroxymethyl)-2H-pyran-3(6H)-one.
    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:0016836    hydro-lyase activity    Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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.

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  4a7y
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  AUD_PHACH | P84193
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  4.2.1.110
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 Related Entries

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

UniProtKB/Swiss-Prot
        AUD_PHACH | P84193: 4a7k 4a7z

(-) Related Entries Specified in the PDB File

4a7k BIFUNCTIONAL ALDOS-2-ULOSE DEHYDRATASE
4a7z COMPLEX OF BIFUNCTIONAL ALDOS-2-ULOSE DEHYDRATASE WITH THE REACTION INTERMEDIATE ASCOPYRONE M