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(-) Description

Title :  STRUCTURE OF AMINOALDEHYDE DEHYDROGENASE 1 FROM SOLANUM LYCOPERSIUM (SLAMADH1) WITH A THIOHEMIACETAL INTERMEDIATE
 
Authors :  S. Morera, A. Vigouroux, D. Kopecny
Date :  05 Dec 12  (Deposition) - 20 Feb 13  (Release) - 01 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aldh10 Family Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kopecny, R. Koncitikova, M. Tylichova, A. Vigouroux, H. Moskalikova, M. Soural, M. Sebela, S. Morera
Plant Aldh10 Family: Identifying Critical Residues For Substrate Specificity And Trapping A Thiohemiacetal Intermediate.
J. Biol. Chem. V. 288 9491 2013
PubMed-ID: 23408433  |  Reference-DOI: 10.1074/JBC.M112.443952

(-) Compounds

Molecule 1 - PUTATIVE BETAINE ALDEHYDE DEHYROGENASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCDFDUET
    Expression System Strain: BL21 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SOLYC06G071290.2
    Organism Common: TOMATO
    Organism Scientific: SOLANUM LYCOPERSICUM
    Organism Taxid: 4081
    Synonym: AMINOALDEHYDE DEHYDROGENASE, AMADH

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
11KA2Ligand/Ion(2-HYDROXYETHOXY)ACETALDEHYDE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3NA2Ligand/IonSODIUM ION
4NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
5PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:158 , THR A:159 , TRP A:161 , LYS A:185 , PRO A:186 , SER A:187 , GLU A:188 , GLY A:218 , GLY A:222 , GLY A:223 , PHE A:236 , GLY A:238 , SER A:239 , THR A:242 , ILE A:246 , HOH A:753 , HOH A:873BINDING SITE FOR RESIDUE NAD A 601
2AC2SOFTWAREILE A:31 , ASP A:99 , LEU A:189 , HOH A:778 , HOH A:866BINDING SITE FOR RESIDUE NA A 602
3AC3SOFTWARETHR A:382 , ASP A:383 , VAL A:384 , VAL A:402 , THR A:404 , HOH A:832BINDING SITE FOR RESIDUE PEG A 603
4AC4SOFTWARETYR B:143BINDING SITE FOR RESIDUE EDO A 604
5AC5SOFTWAREASN A:162 , TYR A:163 , CYS A:295 , SER A:296BINDING SITE FOR RESIDUE 1KA A 605
6AC6SOFTWAREILE B:158 , THR B:159 , TRP B:161 , LYS B:185 , PRO B:186 , SER B:187 , GLU B:188 , GLY B:218 , GLY B:222 , GLY B:223 , PHE B:236 , GLY B:238 , SER B:239 , THR B:242 , ILE B:246 , HOH B:840 , HOH B:970 , HOH B:971 , HOH B:979 , HOH B:994BINDING SITE FOR RESIDUE NAD B 601
7AC7SOFTWAREILE B:31 , ASP B:99 , LEU B:189 , HOH B:733 , HOH B:857BINDING SITE FOR RESIDUE NA B 602
8AC8SOFTWARETYR A:143 , THR B:454 , PHE B:455 , HOH B:810BINDING SITE FOR RESIDUE PEG B 603
9AC9SOFTWAREASN B:162 , TYR B:163 , CYS B:295 , SER B:296 , TRP B:460 , HOH B:737BINDING SITE FOR RESIDUE 1KA B 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I9B)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val B:6 -Pro B:7

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I9B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I9B)

(-) Exons   (0, 0)

(no "Exon" information available for 4I9B)

(-) 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:496
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4i9ba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eee......eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee......eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh.....eee...hhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhh....eeee....eeeee.....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh..eeee................eeee.....hhhhhh.....eeeeeee.hhhhhhhhhh........eee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i9b A   6 VPIPRRQLYIGGEWREPVKKNRIPIINPATEEIIGDIPAATAEDVDIAVEAARKAIARDDWGSTTGAQRAKYLRAIAAKVLEKKSVLATLESLDSGKTLYESAADMDDVAGCFEYYAGLAEALDSRRMTPVNLNSDSYKSYVLREPLGVVGLITPWNYPLLMAIWKVAPALAAGCAAILKPSELASITCLELGEICREIGLPSGALNILTGLGPEAGGPLASHPHVDKISFTGSGPTGSKIMTAAAQLVKPVSLELGGKSPIVVFDDIDNLDIAAEWTLFGIFANTGQVCSATSRLIVQENIASAFMDRLLKWTKNIKISDPLEEDCKLGPVVSAGQYEKVLKFISNAKSEGATILCGGERPQHLKKGYYVQPTIITDVNTSMEIWKEEVFGPVLCVKTFKTEEQAIELANDTKYGLGAAVMSKDVKRCERFTKAFQTGIIWINCSQPTFNELPWGGKKRSGFGRDLGKWGLENFLNIKQVTEYTSAEPLAFYKSP 501
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495      


Chain B from PDB  Type:PROTEIN  Length:496
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4i9bb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eee......eeeee......eeeeee..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee......eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh......eee...hhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhh....eeee....eeeee.....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh...eeee................eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh.......eee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i9b B   6 VPIPRRQLYIGGEWREPVKKNRIPIINPATEEIIGDIPAATAEDVDIAVEAARKAIARDDWGSTTGAQRAKYLRAIAAKVLEKKSVLATLESLDSGKTLYESAADMDDVAGCFEYYAGLAEALDSRRMTPVNLNSDSYKSYVLREPLGVVGLITPWNYPLLMAIWKVAPALAAGCAAILKPSELASITCLELGEICREIGLPSGALNILTGLGPEAGGPLASHPHVDKISFTGSGPTGSKIMTAAAQLVKPVSLELGGKSPIVVFDDIDNLDIAAEWTLFGIFANTGQVCSATSRLIVQENIASAFMDRLLKWTKNIKISDPLEEDCKLGPVVSAGQYEKVLKFISNAKSEGATILCGGERPQHLKKGYYVQPTIITDVNTSMEIWKEEVFGPVLCVKTFKTEEQAIELANDTKYGLGAAVMSKDVKRCERFTKAFQTGIIWINCSQPTFNELPWGGKKRSGFGRDLGKWGLENFLNIKQVTEYTSAEPLAFYKSP 501
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495
   Legend:   → Mismatch (orange background)
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    → 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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I9B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I9B)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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        Q56R04_SOLLC | Q56R04: 4i8q

(-) Related Entries Specified in the PDB File

3iwj 3iwk 4i8p 4i8q