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(-) Description

Title :  X-RAY STRUCTURE OF BINARY-SECOISOLARICIRESINOL DEHYDROGENASE
 
Authors :  B. Youn, S. G. Moinuddin, L. B. Davin, N. G. Lewis, C. Kang
Date :  23 Dec 04  (Deposition) - 13 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Xidoreductase, Oxidoreductase, Dehydrogenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Youn, S. G. Moinuddin, L. B. Davin, N. G. Lewis, C. Kang
Crystal Structures Of Apo-Form And Binary/Ternary Complexes Of Podophyllum Secoisolariciresinol Dehydrogenase, An Enzyme Involved In Formation Of Health-Protecting And Plant Defense Lignans
J. Biol. Chem. V. 280 12917 2005
PubMed-ID: 15653677  |  Reference-DOI: 10.1074/JBC.M413266200

(-) Compounds

Molecule 1 - RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCHIS2-TOPO TA VECTOR
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Organism Common: MAYAPPLE
    Organism Scientific: PODOPHYLLUM PELTATUM
    Organism Taxid: 35933

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAJ1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDICFORM)
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1NAJ4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDICFORM)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:23 , GLY A:26 , GLY A:27 , ILE A:28 , ASP A:47 , ILE A:48 , CYS A:71 , ASP A:72 , VAL A:73 , THR A:74 , ASN A:99 , VAL A:100 , GLY A:101 , ILE A:124 , THR A:151 , ALA A:152 , SER A:153 , TYR A:167 , LYS A:171 , TYR A:198 , ILE A:199 , VAL A:200BINDING SITE FOR RESIDUE NAJ A1300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BGL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BGL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BGL)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.SILD_PODPE154-182  1A:154-182
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.SILD_PODPE154-182  4A:154-182

(-) Exons   (0, 0)

(no "Exon" information available for 2BGL)

(-) 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:267
 aligned with SILD_PODPE | Q94KL8 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:267
                                    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       270       
           SILD_PODPE    11 TNRLQDKVAIITGGAGGIGETTAKLFVRYGAKVVIADIADDHGQKVCNNIGSPDVISFVHCDVTKDEDVRNLVDTTIAKHGKLDIMFGNVGVLSTTPYSILEAGNEDFKRVMDINVYGAFLVAKHAARVMIPAKKGSIVFTASISSFTAGEGVSHVYTATKHAVLGLTTSLCTELGEYGIRVNCVSPYIVASPLLTDVFGVDSSRVEELAHQAANLKGTLLRAEDVADAVAYLAGDESKYVSGLNLVIDGGYTRTNPAFPTALKHGL 277
               SCOP domains d2bgla_ A: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....hhhhhhhhhhh....eee........hhhhhh.......ee.......hhhhhhhhhhhhhhhh....eee.....................hhhhhh...hhhhhhhhhhhhhhhhh.eeee................hhhhhhhhh...............eeeeeee....................................hhhhhhhhhhhh..........eee...hhhhh...hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:154-182    ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bgl A  11 TNRLQDKVAIITGGAGGIGETTAKLFVRYGAKVVIADIADDHGQKVCNNIGSPDVISFVHCDVTKDEDVRNLVDTTIAKHGKLDIMFGNVGVLSTTPYSILEAGNEDFKRVMDINVYGAFLVAKHAARVMIPAKKGSIVFTASISSFTAGEGVSHVYTATKHAVLGLTTSLCTELGEYGIRVNCVSPYIVASPLLTDVFGVDSSRVEELAHQAANLKGTLLRAEDVADAVAYLAGDESKYVSGLNLVIDGGYTRTNPAFPTALKHGL 277
                                    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       270
   Legend:   → Mismatch (orange background)
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  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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BGL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BGL)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (SILD_PODPE | Q94KL8)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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
        SILD_PODPE | Q94KL8: 2bgk 2bgm

(-) Related Entries Specified in the PDB File

2bgk X-RAY STRUCTURE OF APO-SECOISOLARICIRESINOL DEHYDROGENASE
2bgm X-RAY STRUCTURE OF TERNARY- SECOISOLARICIRESINOL DEHYDROGENASE