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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINOALDEHYDE DEHYDROGENASE 2 FROM PISUM SATIVUM (PSAMADH2)
 
Authors :  D. Kopecny, S. Morera, P. Briozzo
Date :  02 Sep 09  (Deposition) - 19 Jan 10  (Release) - 04 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Dimer, Aminoaldehyde Dehydrogenase, Betaine Aldehyde Dehydrogenase, Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Tylichova, D. Kopecny, S. Morera, P. Briozzo, R. Lenobel, J. Snegaroff, M. Sebela
Structural And Functional Characterization Of Plant Aminoaldehyde Dehydrogenase From Pisum Sativum With A Broad Specificity For Natural And Synthetic Aminoaldehydes.
J. Mol. Biol. V. 396 870 2010
PubMed-ID: 20026072  |  Reference-DOI: 10.1016/J.JMB.2009.12.015

(-) Compounds

Molecule 1 - PUTATIVE AMINOALDEHYDE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.2.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCDFDUET
    Expression System Strain: T7
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AMADH2
    Organism Common: GARDEN PEA
    Organism Scientific: PISUM SATIVUM
    Organism Taxid: 3888

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2NA2Ligand/IonSODIUM ION
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE 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 , ALA A:223 , PHE A:236 , GLY A:238 , SER A:239 , THR A:242 , ILE A:246 , HOH A:555 , HOH A:580BINDING SITE FOR RESIDUE NAD A 504
02AC2SOFTWAREILE A:28 , ASP A:99 , LEU A:189 , HOH A:562 , HOH A:572BINDING SITE FOR RESIDUE NA A 505
03AC3SOFTWAREASP A:110 , ASP A:113 , CYS A:453 , HOH A:602BINDING SITE FOR RESIDUE GOL A 506
04AC4SOFTWAREASN A:162 , TYR A:163 , TRP A:170 , ILE A:293 , CYS A:294 , TRP A:459BINDING SITE FOR RESIDUE GOL A 507
05AC5SOFTWAREGLU A:473 , ASP A:477 , ARG B:149BINDING SITE FOR RESIDUE GOL A 508
06AC6SOFTWAREILE 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 , ALA B:223 , PHE B:236 , SER B:239 , THR B:242 , ILE B:246 , HOH B:544 , HOH B:575 , HOH B:610BINDING SITE FOR RESIDUE NAD B 504
07AC7SOFTWAREILE B:28 , ASP B:99 , LEU B:189 , HOH B:526 , HOH B:537BINDING SITE FOR RESIDUE NA B 505
08AC8SOFTWAREASP B:113 , TYR B:163 , LEU B:166 , CYS B:453 , GOL B:508 , HOH B:658BINDING SITE FOR RESIDUE GOL B 506
09AC9SOFTWAREARG A:149 , HOH A:599 , GLU B:473 , TRP B:474 , ASP B:477BINDING SITE FOR RESIDUE GOL B 507
10BC1SOFTWARETYR B:163 , TRP B:170 , ILE B:293 , CYS B:294 , SER B:295 , TRP B:459 , GOL B:506BINDING SITE FOR RESIDUE GOL B 508
11BC2SOFTWARELYS B:44 , THR B:227 , HOH B:590 , HOH B:618BINDING SITE FOR RESIDUE GOL B 509

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IWJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IWJ)

(-) 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
 aligned with Q93YB2_PEA | Q93YB2 from UniProtKB/TrEMBL  Length:503

    Alignment length:500
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503
           Q93YB2_PEA     4 PIPTRQLFINGDWKAPVLNKRIPVINPATQNIIGDIPAATKEDVDVAVAAAKTALTRNKGADWATASGAVRARYLRAIAAKVTEKKPELAKLESIDCGKPLDEAAWDIDDVAGCFEYYADLAEKLDARQKAPVSLPMDTFKSHVLREPIGVVGLITPWNYPMLMATWKVAPALAAGCAAILKPSELASLTCLELGEICKEVGLPPGVLNILTGLGPEAGAPLATHPDVDKVAFTGSSATGSKIMTAAAQLVKPVSLELGGKSPLVVFEDVDLDKAAEWAIFGCFWTNGQICSATSRLILHESIATEFLNRIVKWIKNIKISDPLEEGCRLGPVVSEGQYEKILKFVSNAKSEGATILTGGSRPEHLKKGFFIEPTIITDVTTNMQIWREEVFGPVLCVKTFSTEEEAIDLANDTVYGLGAAVISNDLERCERVTKAFKAGIVWVNCSQPCFTQAPWGGVKRSGFGRELGEWGLDNYLSVKQVTQYISEEPWGWYQPPAKL 503
               SCOP domains d3iwja_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3iwjA02 A:263-454 Aldehyde Dehydrogenase; Chain A, domain 2                                                                                                                                     ------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee......eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh.....eee...hhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhh..eeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh..eeee................eeee.....hhhhhh.....eeeeeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iwj A   4 PIPTRQLFINGDWKAPVLNKRIPVINPATQNIIGDIPAATKEDVDVAVAAAKTALTRNKGADWATASGAVRARYLRAIAAKVTEKKPELAKLESIDCGKPLDEAAWDIDDVAGCFEYYADLAEKLDARQKAPVSLPMDTFKSHVLREPIGVVGLITPWNYPMLMATWKVAPALAAGCAAILKPSELASLTCLELGEICKEVGLPPGVLNILTGLGPEAGAPLATHPDVDKVAFTGSSATGSKIMTAAAQLVKPVSLELGGKSPLVVFEDVDLDKAAEWAIFGCFWTNGQICSATSRLILHESIATEFLNRIVKWIKNIKISDPLEEGCRLGPVVSEGQYEKILKFVSNAKSEGATILTGGSRPEHLKKGFFIEPTIITDVTTNMQIWREEVFGPVLCVKTFSTEEEAIDLANDTVYGLGAAVISNDLERCERVTKAFKAGIVWVNCSQPCFTQAPWGGVKRSGFGRELGEWGLDNYLSVKQVTQYISEEPWGWYQPPAKL 503
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503


Chain B from PDB  Type:PROTEIN  Length:500
 aligned with Q93YB2_PEA | Q93YB2 from UniProtKB/TrEMBL  Length:503

    Alignment length:500
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503
           Q93YB2_PEA     4 PIPTRQLFINGDWKAPVLNKRIPVINPATQNIIGDIPAATKEDVDVAVAAAKTALTRNKGADWATASGAVRARYLRAIAAKVTEKKPELAKLESIDCGKPLDEAAWDIDDVAGCFEYYADLAEKLDARQKAPVSLPMDTFKSHVLREPIGVVGLITPWNYPMLMATWKVAPALAAGCAAILKPSELASLTCLELGEICKEVGLPPGVLNILTGLGPEAGAPLATHPDVDKVAFTGSSATGSKIMTAAAQLVKPVSLELGGKSPLVVFEDVDLDKAAEWAIFGCFWTNGQICSATSRLILHESIATEFLNRIVKWIKNIKISDPLEEGCRLGPVVSEGQYEKILKFVSNAKSEGATILTGGSRPEHLKKGFFIEPTIITDVTTNMQIWREEVFGPVLCVKTFSTEEEAIDLANDTVYGLGAAVISNDLERCERVTKAFKAGIVWVNCSQPCFTQAPWGGVKRSGFGRELGEWGLDNYLSVKQVTQYISEEPWGWYQPPAKL 503
               SCOP domains d3iwjb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3iwjB02 B:263-454 Aldehyde Dehydrogenase; Chain A, domain 2                                                                                                                                     ------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee......eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh.....eee...hhhhhhhhhh......eeeee.hhhhhhhhhhhhhh....eeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh..eeee................eeee.....hhhhhh.....eeeeeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iwj B   4 PIPTRQLFINGDWKAPVLNKRIPVINPATQNIIGDIPAATKEDVDVAVAAAKTALTRNKGADWATASGAVRARYLRAIAAKVTEKKPELAKLESIDCGKPLDEAAWDIDDVAGCFEYYADLAEKLDARQKAPVSLPMDTFKSHVLREPIGVVGLITPWNYPMLMATWKVAPALAAGCAAILKPSELASLTCLELGEICKEVGLPPGVLNILTGLGPEAGAPLATHPDVDKVAFTGSSATGSKIMTAAAQLVKPVSLELGGKSPLVVFEDVDLDKAAEWAIFGCFWTNGQICSATSRLILHESIATEFLNRIVKWIKNIKISDPLEEGCRLGPVVSEGQYEKILKFVSNAKSEGATILTGGSRPEHLKKGFFIEPTIITDVTTNMQIWREEVFGPVLCVKTFSTEEEAIDLANDTVYGLGAAVISNDLERCERVTKAFKAGIVWVNCSQPCFTQAPWGGVKRSGFGRELGEWGLDNYLSVKQVTQYISEEPWGWYQPPAKL 503
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q93YB2_PEA | Q93YB2)
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.
    GO:0016620    oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
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.
    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

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3iwk