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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NADP-DEPENDENT MANNITOL DEHYDROGENASE FROM CLADOSPORIUM HERBARUM.
 
Authors :  D. Nuess, P. Goettig, I. Magler, U. Denk, M. Breitenbach, P. B. Schneide H. Brandstetter, B. Simon-Nobbe
Date :  24 Feb 09  (Deposition) - 26 May 10  (Release) - 04 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rossmann Fold, Beta-Alpha-Beta Motifs, Open Twisted Sheet, Allergen, Nadp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Nuss, P. Goettig, I. Magler, U. Denk, M. Breitenbach, P. B. Schneider, H. Brandstetter, B. Simon-Nobbe
Crystal Structure Of The Nadp-Dependent Mannitol Dehydrogenase From Cladosporium Herbarum: Implications For Oligomerisation And Catalysis.
Biochimie V. 92 985 2010
PubMed-ID: 20420880  |  Reference-DOI: 10.1016/J.BIOCHI.2010.04.012

(-) Compounds

Molecule 1 - PROBABLE NADP-DEPENDENT MANNITOL DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.138
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS-PARALLEL2
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: CLADOSPORIUM HERBARUM
    Organism Taxid: 29918
    Synonym: MTDH, MANNITOL 2-DEHYDROGENASE [NADP+]

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:123 , HIS A:127 , GLU D:86 , GLU D:89BINDING SITE FOR RESIDUE ZN A 1003
2AC2SOFTWAREARG A:267 , HOH A:376 , HOH A:551 , ARG D:267 , HOH D:366BINDING SITE FOR RESIDUE ZN A 1004
3AC3SOFTWAREARG B:267 , ARG C:267 , HOH C:349 , HOH C:436 , HOH C:552BINDING SITE FOR RESIDUE ZN B 1001
4AC4SOFTWAREGLU B:123 , HIS B:127 , GLU C:86 , GLU C:89BINDING SITE FOR RESIDUE ZN B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GDF)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Met A:1 -Pro A:2
2Phe B:168 -Pro B:169
3Phe C:168 -Pro C:169

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GDF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GDF)

(-) Exons   (0, 0)

(no "Exon" information available for 3GDF)

(-) 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:267
 aligned with MTDH_DAVTA | P0C0Y5 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:267
                                    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       
           MTDH_DAVTA     1 MPGQQATKHESLLDQLSLKGKVVVVTGASGPKGMGIEAARGCAEMGAAVAITYASRAQGAEENVKELEKTYGIKAKAYKCQVDSYESCEKLVKDVVADFGQIDAFIANAGATADSGILDGSVEAWNHVVQVDLNGTFHCAKAVGHHFKERGTGSLVITASMSGHIANFPQEQTSYNVAKAGCIHMARSLANEWRDFARVNSISPGYIDTGLSDFVPKETQQLWHSMIPMGRDGLAKELKGAYVYFASDASTYTTGADLLIDGGYTTR 267
               SCOP domains d3gdfa_ A: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhh....eeee.......hhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhh....eeeeeee..ee..hhhhhhhhhhhhhhhhh.....ee...hhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gdf A   1 MPGQQATKHESLLDQLSLKGKVVVVTGASGPKGMGIEAARGCAEMGAAVAITYASRAQGAEENVKELEKTYGIKAKAYKCQVDSYESCEKLVKDVVADFGQIDAFIANAGATADSGILDGSVEAWNHVVQVDLNGTFHCAKAVGHHFKERGTGSLVITASMSGHIANFPQEQTSYNVAKAGCIHMARSLANEWRDFARVNSISPGYIDTGLSDFVPKETQQLWHSMIPMGRDGLAKELKGAYVYFASDASTYTTGADLLIDGGYTTR 267
                                    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       


Chain B from PDB  Type:PROTEIN  Length:267
 aligned with MTDH_DAVTA | P0C0Y5 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:267
                                    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       
           MTDH_DAVTA     1 MPGQQATKHESLLDQLSLKGKVVVVTGASGPKGMGIEAARGCAEMGAAVAITYASRAQGAEENVKELEKTYGIKAKAYKCQVDSYESCEKLVKDVVADFGQIDAFIANAGATADSGILDGSVEAWNHVVQVDLNGTFHCAKAVGHHFKERGTGSLVITASMSGHIANFPQEQTSYNVAKAGCIHMARSLANEWRDFARVNSISPGYIDTGLSDFVPKETQQLWHSMIPMGRDGLAKELKGAYVYFASDASTYTTGADLLIDGGYTTR 267
               SCOP domains d3gdfb_ B: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhh....eeee.......hhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhh....eeeeeee..ee..hhhhhhhhhhhhhhhhh.....ee...hhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gdf B   1 MPGQQATKHESLLDQLSLKGKVVVVTGASGPKGMGIEAARGCAEMGAAVAITYASRAQGAEENVKELEKTYGIKAKAYKCQVDSYESCEKLVKDVVADFGQIDAFIANAGATADSGILDGSVEAWNHVVQVDLNGTFHCAKAVGHHFKERGTGSLVITASMSGHIANFPQEQTSYNVAKAGCIHMARSLANEWRDFARVNSISPGYIDTGLSDFVPKETQQLWHSMIPMGRDGLAKELKGAYVYFASDASTYTTGADLLIDGGYTTR 267
                                    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       


Chain C from PDB  Type:PROTEIN  Length:267
 aligned with MTDH_DAVTA | P0C0Y5 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:267
                                    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       
           MTDH_DAVTA     1 MPGQQATKHESLLDQLSLKGKVVVVTGASGPKGMGIEAARGCAEMGAAVAITYASRAQGAEENVKELEKTYGIKAKAYKCQVDSYESCEKLVKDVVADFGQIDAFIANAGATADSGILDGSVEAWNHVVQVDLNGTFHCAKAVGHHFKERGTGSLVITASMSGHIANFPQEQTSYNVAKAGCIHMARSLANEWRDFARVNSISPGYIDTGLSDFVPKETQQLWHSMIPMGRDGLAKELKGAYVYFASDASTYTTGADLLIDGGYTTR 267
               SCOP domains d3gdfc_ C: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhh....eeee.......hhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhh....eeeeeee..ee..hhhhhhhhhhhhhhhhh.....ee...hhhhhhhhhhhhhh....eeeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gdf C   1 MPGQQATKHESLLDQLSLKGKVVVVTGASGPKGMGIEAARGCAEMGAAVAITYASRAQGAEENVKELEKTYGIKAKAYKCQVDSYESCEKLVKDVVADFGQIDAFIANAGATADSGILDGSVEAWNHVVQVDLNGTFHCAKAVGHHFKERGTGSLVITASMSGHIANFPQEQTSYNVAKAGCIHMARSLANEWRDFARVNSISPGYIDTGLSDFVPKETQQLWHSMIPMGRDGLAKELKGAYVYFASDASTYTTGADLLIDGGYTTR 267
                                    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       


Chain D from PDB  Type:PROTEIN  Length:267
 aligned with MTDH_DAVTA | P0C0Y5 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:267
                                    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       
           MTDH_DAVTA     1 MPGQQATKHESLLDQLSLKGKVVVVTGASGPKGMGIEAARGCAEMGAAVAITYASRAQGAEENVKELEKTYGIKAKAYKCQVDSYESCEKLVKDVVADFGQIDAFIANAGATADSGILDGSVEAWNHVVQVDLNGTFHCAKAVGHHFKERGTGSLVITASMSGHIANFPQEQTSYNVAKAGCIHMARSLANEWRDFARVNSISPGYIDTGLSDFVPKETQQLWHSMIPMGRDGLAKELKGAYVYFASDASTYTTGADLLIDGGYTTR 267
               SCOP domains d3gdfd_ D: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhh....eeee.......hhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhh....eeeeeee..ee.......hhhhhhhhhhhh.....ee...hhhhhhhhhh.........eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gdf D   1 MPGQQATKHESLLDQLSLKGKVVVVTGASGPKGMGIEAARGCAEMGAAVAITYASRAQGAEENVKELEKTYGIKAKAYKCQVDSYESCEKLVKDVVADFGQIDAFIANAGATADSGILDGSVEAWNHVVQVDLNGTFHCAKAVGHHFKERGTGSLVITASMSGHIANFPQEQTSYNVAKAGCIHMARSLANEWRDFARVNSISPGYIDTGLSDFVPKETQQLWHSMIPMGRDGLAKELKGAYVYFASDASTYTTGADLLIDGGYTTR 267
                                    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
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GDF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GDF)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (MTDH_DAVTA | P0C0Y5)
molecular function
    GO:0050085    mannitol 2-dehydrogenase (NADP+) activity    Catalysis of the reaction: D-mannitol + NADP(+) = D-fructose + H(+) + NADPH.
    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.
biological process
    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
        MTDH_DAVTA | P0C0Y5: 3gdg

(-) Related Entries Specified in the PDB File

3gdg