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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINOALDEHYDE DEHYDROGENASE 1A FROM ZEA MAYS (ZMAMADH1A)
 
Authors :  S. Morera, A. Vigouroux, D. Kopecny
Date :  04 Dec 12  (Deposition) - 20 Feb 13  (Release) - 01 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
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 - AMINOALDEHYDE DEHYDROGENASE 1
    Chains: A, B
    EC Number: 1.2.1.19
    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: AMADH1
    Organism Common: MAIZE
    Organism Scientific: ZEA MAYS
    Organism Taxid: 4577
    Synonym: AMADH

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3NA2Ligand/IonSODIUM ION
4NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:160 , THR A:161 , PRO A:162 , TRP A:163 , ASN A:164 , LYS A:187 , PRO A:188 , SER A:189 , GLU A:190 , GLY A:220 , GLY A:224 , ALA A:225 , PHE A:238 , THR A:239 , GLY A:240 , SER A:241 , THR A:244 , LYS A:247 , ILE A:248 , GLU A:262 , LEU A:263 , GLY A:264 , CYS A:296 , GLU A:395 , PHE A:397 , LEU A:423 , TRP A:461 , HOH A:709 , HOH A:826 , HOH A:837 , HOH A:842 , HOH A:937 , HOH A:957 , HOH A:1085BINDING SITE FOR RESIDUE NAD A 601
2AC2SOFTWAREVAL A:30 , ASP A:101 , LEU A:191 , HOH A:701 , HOH A:919BINDING SITE FOR RESIDUE NA A 602
3AC3SOFTWAREPRO A:28 , GLU A:190 , LEU A:219 , HOH A:1021BINDING SITE FOR RESIDUE GOL A 603
4AC4SOFTWARETRP A:172 , CYS A:296 , SER A:297 , HOH A:810 , HOH A:898BINDING SITE FOR RESIDUE EDO A 604
5AC5SOFTWAREILE B:160 , THR B:161 , PRO B:162 , TRP B:163 , ASN B:164 , LYS B:187 , PRO B:188 , SER B:189 , GLU B:190 , GLY B:220 , GLY B:224 , ALA B:225 , PHE B:238 , THR B:239 , GLY B:240 , SER B:241 , THR B:244 , ILE B:248 , GLU B:262 , LEU B:263 , GLY B:264 , CYS B:296 , GLU B:395 , PHE B:397 , TRP B:461 , HOH B:713 , HOH B:720 , HOH B:731 , HOH B:813 , HOH B:814BINDING SITE FOR RESIDUE NAD B 601
6AC6SOFTWAREVAL B:30 , ASP B:101 , LEU B:191 , HOH B:773 , HOH B:845BINDING SITE FOR RESIDUE NA B 602
7AC7SOFTWARELYS B:355 , ILE B:361 , GLY B:364 , GLY B:365 , HOH B:865BINDING SITE FOR RESIDUE PEG B 603
8AC8SOFTWARETYR B:165 , TRP B:172 , TRP B:290 , CYS B:296 , SER B:297 , TRP B:461 , HOH B:921 , HOH B:981 , HOH B:1005BINDING SITE FOR RESIDUE EDO B 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I8P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4I8P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I8P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I8P)

(-) Exons   (0, 0)

(no "Exon" information available for 4I8P)

(-) 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:500
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4i8pa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee......eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.......eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh......eee.......hhhhhhh.....eeeee.hhhhhhhhhhhhhhhh..eeee.....eeee....hhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh..eeee................eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee..............hhh.ee......hhhhh.eeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i8p A   6 MVPLRQLFVDGEWRPPAQGRRLPVVNPTTEAHIGEIPAGTAEDVDAAVAAARAALKRNRGRDWARAPGAVRAKYLRAIAAKVIERKPELAKLEALDCGKPYDEAAWDMDDVAGCFEYFADQAEALDKRQNSPVSLPMETFKCHLRREPIGVVGLITPWNYPLLMATWKIAPALAAGCTAVLKPSELASVTCLELADICKEVGLPSGVLNIVTGLGPDAGAPLSAHPDVDKVAFTGSFETGKKIMASAAPMVKPVTLELGGKSPIVVFDDVDIDKAVEWTLFGCFWTNGQICSATSRLLIHTKIAKKFNERMVAWAKNIKVSDPLEEGCRLGPVVSEGQYEKIKKFISNAKSQGATILTGGVRPAHLEKGFFIEPTIITDITTSMEIWREEVFGPVLCVKEFSTEDEAIELANDTQYGLAGAVISGDRERCQRLSEEIDAGCIWVNCSQPCFCQAPWGGNKRSGFGRELGEGGIDNYLSVKQVTEYISDEPWGWYQSPSKL 505
                                    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       505


Chain B from PDB  Type:PROTEIN  Length:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4i8pb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee..eee......eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeee..eeeee....hhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh.....eee...hhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh..eeee.....eeee....hhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh..eeee................eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee..............hhh.ee.......hhhh.eeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4i8p B   6 MVPLRQLFVDGEWRPPAQGRRLPVVNPTTEAHIGEIPAGTAEDVDAAVAAARAALKRNRGRDWARAPGAVRAKYLRAIAAKVIERKPELAKLEALDCGKPYDEAAWDMDDVAGCFEYFADQAEALDKRQNSPVSLPMETFKCHLRREPIGVVGLITPWNYPLLMATWKIAPALAAGCTAVLKPSELASVTCLELADICKEVGLPSGVLNIVTGLGPDAGAPLSAHPDVDKVAFTGSFETGKKIMASAAPMVKPVTLELGGKSPIVVFDDVDIDKAVEWTLFGCFWTNGQICSATSRLLIHTKIAKKFNERMVAWAKNIKVSDPLEEGCRLGPVVSEGQYEKIKKFISNAKSQGATILTGGVRPAHLEKGFFIEPTIITDITTSMEIWREEVFGPVLCVKEFSTEDEAIELANDTQYGLAGAVISGDRERCQRLSEEIDAGCIWVNCSQPCFCQAPWGGNKRSGFGRELGEGGIDNYLSVKQVTEYISDEPWGWYQSPS 503
                                    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)
  - → 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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I8P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I8P)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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(-) Related Entries Specified in the PDB File

3iwj 3iwk 4i8q