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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALDH3A1 MODIFIED WITH THE BETA-ELIMINATION PRODUCT OF ALDI-1; 1-PHENYL- 2-PROPEN-1-ONE
 
Authors :  M. Khanna, T. D. Hurley
Date :  18 Jul 11  (Deposition) - 02 Nov 11  (Release) - 28 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.51
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aldh, Aldi-1, Inhibitor, Rossmann Fold, Covalent Adduct, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Khanna, C. H. Chen, A. Kimble-Hill, B. Parajuli, S. Perez-Miller, S. Baskaran, J. Kim, K. Dria, V. Vasiliou, D. Mochly-Rosen, T. D. Hurle
Discovery Of A Novel Class Of Covalent Inhibitor For Aldehyde Dehydrogenases.
J. Biol. Chem. V. 286 43486 2011
PubMed-ID: 22021038  |  Reference-DOI: 10.1074/JBC.M111.293597
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALDEHYDE DEHYDROGENASE
    ChainsA, B
    EC Number1.2.1.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneALDH3A1, ALDH3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymALDHIII, ALDEHYDE DEHYDROGENASE 3, ALDEHYDE DEHYDROGENASE FAMILY 3 MEMBER A1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2I1E2Ligand/Ion1-PHENYLPROPAN-1-ONE
3K4Ligand/IonPOTASSIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:277 , THR A:321 , ASP A:322 , HOH A:459 , HOH A:643 , HOH A:669 , HOH A:870BINDING SITE FOR RESIDUE K A 602
2AC2SOFTWARELYS A:439 , TYR A:442 , HOH A:562 , HOH B:1012BINDING SITE FOR RESIDUE K A 603
3AC3SOFTWAREASN A:434 , ASP A:435 , LYS A:439 , TYR A:442 , HOH A:513 , ARG B:230BINDING SITE FOR RESIDUE ACT A 701
4AC4SOFTWAREGLU A:61 , ASN A:114 , TYR A:115 , CYS A:243 , HOH A:636 , HOH A:949BINDING SITE FOR RESIDUE I1E A 1001
5AC5SOFTWAREGLU B:79 , TRP B:80 , ALA B:82 , HOH B:521 , HOH B:556BINDING SITE FOR RESIDUE K B 601
6AC6SOFTWARELYS B:439 , TYR B:442 , HOH B:460 , HOH B:754 , HOH B:802 , HOH B:911BINDING SITE FOR RESIDUE K B 603
7AC7SOFTWAREARG A:230 , ASN B:434 , ASP B:435 , LYS B:439 , TYR B:442 , HOH B:467BINDING SITE FOR RESIDUE ACT B 701
8AC8SOFTWAREASN B:114 , TYR B:115 , THR B:242 , CYS B:243 , ILE B:394 , HOH B:790 , HOH B:1005BINDING SITE FOR RESIDUE I1E B 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:443 -Pro A:444
2Pro B:443 -Pro B:444

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018981S134AAL3A1_HUMANPolymorphism887241A/BA133A
2UniProtVAR_018982G309EAL3A1_HUMANPolymorphism3744692A/BG308E
3UniProtVAR_011303P329AAL3A1_HUMANPolymorphism2228100A/BP328A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDEHYDE_DEHYDR_GLUPS00687 Aldehyde dehydrogenases glutamic acid active site.AL3A1_HUMAN209-216
 
  2A:208-215
B:208-215
2ALDEHYDE_DEHYDR_CYSPS00070 Aldehyde dehydrogenases cysteine active site.AL3A1_HUMAN237-248
 
  2A:236-247
B:236-247

(-) Exons   (0, 0)

(no "Exon" information available for 3SZB)

(-) 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:447
 aligned with AL3A1_HUMAN | P30838 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:447
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       
          AL3A1_HUMAN     2 SKISEAVKRARAAFSSGRTRPLQFRIQQLEALQRLIQEQEQELVGALAADLHKNEWNAYYEEVVYVLEEIEYMIQKLPEWAADEPVEKTPQTQQDELYIHSEPLGVVLVIGTWNYPFNLTIQPMVGAIAAGNSVVLKPSELSENMASLLATIIPQYLDKDLYPVINGGVPETTELLKERFDHILYTGSTGVGKIIMTAAAKHLTPVTLELGGKSPCYVDKNCDLDVACRRIAWGKFMNSGQTCVAPDYILCDPSIQNQIVEKLKKSLKEFYGEDAKKSRDYGRIISARHFQRVMGLIEGQKVAYGGTGDAATRYIAPTILTDVDPQSPVMQEEIFGPVLPIVCVRSLEEAIQFINQREKPLALYMFSSNDKVIKKMIAETSSGGVAANDVIVHITLHSLPFGGVGNSGMGSYHGKKSFETFSHRRSCLVRPLMNDEGLKVRYPPSPA 448
               SCOP domains d3szba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee...hhhhh..eeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh..........hhhhhhhhh.....eeeee.hhhhhhhhhhhhhh....eeee.....eeee....hhhhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhhhhh.hhhhh.......hhhhhhhhhhhhh..eeee...ee....ee..eeee.....hhhhh......eeeeee..hhhhhhhhhhhh....eeeee..hhhhhhhhhhhh...eeee...hhhhh........hhh.ee....hhhhhhhheeeeeeee........hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------------------------------------------------------------------------------E-------------------A----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALDEHYDE--------------------ALDEHYDE_DEH-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3szb A   1 SKISEAVKRARAAFSSGRTRPLQFRIQQLEALQRLIQEQEQELVGALAADLHKNEWNAYYEEVVYVLEEIEYMIQKLPEWAADEPVEKTPQTQQDELYIHSEPLGVVLVIGTWNYPFNLTIQPMVGAIAAGNAVVLKPSELSENMASLLATIIPQYLDKDLYPVINGGVPETTELLKERFDHILYTGSTGVGKIIMTAAAKHLTPVTLELGGKSPCYVDKNCDLDVACRRIAWGKFMNSGQTCVAPDYILCDPSIQNQIVEKLKKSLKEFYGEDAKKSRDYGRIISARHFQRVMGLIEGQKVAYGGTGDAATRYIAPTILTDVDPQSPVMQEEIFGPVLPIVCVRSLEEAIQFINQREKPLALYMFSSNDKVIKKMIAETSSGGVAANDVIVHITLHSLPFGGVGNSGMGSYHGKKSFETFSHRRSCLVRPLMNDEGLKVRYPPSPA 447
                                    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       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       

Chain B from PDB  Type:PROTEIN  Length:452
 aligned with AL3A1_HUMAN | P30838 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:452
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451  
          AL3A1_HUMAN     2 SKISEAVKRARAAFSSGRTRPLQFRIQQLEALQRLIQEQEQELVGALAADLHKNEWNAYYEEVVYVLEEIEYMIQKLPEWAADEPVEKTPQTQQDELYIHSEPLGVVLVIGTWNYPFNLTIQPMVGAIAAGNSVVLKPSELSENMASLLATIIPQYLDKDLYPVINGGVPETTELLKERFDHILYTGSTGVGKIIMTAAAKHLTPVTLELGGKSPCYVDKNCDLDVACRRIAWGKFMNSGQTCVAPDYILCDPSIQNQIVEKLKKSLKEFYGEDAKKSRDYGRIISARHFQRVMGLIEGQKVAYGGTGDAATRYIAPTILTDVDPQSPVMQEEIFGPVLPIVCVRSLEEAIQFINQREKPLALYMFSSNDKVIKKMIAETSSGGVAANDVIVHITLHSLPFGGVGNSGMGSYHGKKSFETFSHRRSCLVRPLMNDEGLKVRYPPSPAKMTQH 453
               SCOP domains d3szbb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee...hhhhh..eeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh..........hhhhhhhhh.....eeeee.hhhhhhhhhhhhhh....eeee.....eeee....hhhhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhhhhh.hhhhh.......hhhhhhhhhhh....eeee...ee....ee..eeee.....hhhhh......eeeeee..hhhhhhhhhhhh....eeeee..hhhhhhhhhhhh...eeee...hhhhh........hhh.ee....hhhhhhhheeeeeeee.....hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------------------------------------------------------------------------------E-------------------A---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALDEHYDE--------------------ALDEHYDE_DEH------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3szb B   1 SKISEAVKRARAAFSSGRTRPLQFRIQQLEALQRLIQEQEQELVGALAADLHKNEWNAYYEEVVYVLEEIEYMIQKLPEWAADEPVEKTPQTQQDELYIHSEPLGVVLVIGTWNYPFNLTIQPMVGAIAAGNAVVLKPSELSENMASLLATIIPQYLDKDLYPVINGGVPETTELLKERFDHILYTGSTGVGKIIMTAAAKHLTPVTLELGGKSPCYVDKNCDLDVACRRIAWGKFMNSGQTCVAPDYILCDPSIQNQIVEKLKKSLKEFYGEDAKKSRDYGRIISARHFQRVMGLIEGQKVAYGGTGDAATRYIAPTILTDVDPQSPVMQEEIFGPVLPIVCVRSLEEAIQFINQREKPLALYMFSSNDKVIKKMIAETSSGGVAANDVIVHITLHSLPFGGVGNSGMGSYHGKKSFETFSHRRSCLVRPLMNDEGLKVRYPPSPAKMTQH 452
                                    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       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450  

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AL3A1_HUMAN | P30838)
molecular function
    GO:0004028    3-chloroallyl aldehyde dehydrogenase activity    Catalysis of the reaction: 3-chloroallyl aldehyde + H2O = 2 H+ + 2 e- + 3-chloroacrylic acid.
    GO:0008106    alcohol dehydrogenase (NADP+) activity    Catalysis of the reaction: an alcohol + NADP+ = an aldehyde + NADPH + H+.
    GO:0004029    aldehyde dehydrogenase (NAD) activity    Catalysis of the reaction: an aldehyde + NAD+ + H2O = an acid + NADH + H+.
    GO:0004030    aldehyde dehydrogenase [NAD(P)+] activity    Catalysis of the reaction: an aldehyde + NAD(P)+ + H2O = an acid + NAD(P)H + H+.
    GO:0018479    benzaldehyde dehydrogenase (NAD+) activity    Catalysis of the reaction: benzaldehyde + NAD+ + H2O = benzoate + NADH + H+.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0006081    cellular aldehyde metabolic process    The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells.
    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.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0051591    response to cAMP    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0051384    response to glucocorticoid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0007584    response to nutrient    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0006805    xenobiotic metabolic process    The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        AL3A1_HUMAN | P308383sza 4h80 4l1o 4l2o

(-) Related Entries Specified in the PDB File

3sz9 CRYSTAL STRUCTURE OF HUMAN ALDH2 MODIFIED WITH THE BETA- ELIMINATION PRODUCT OF ALDI-3; 1-(4-ETHYLBENZENE)PROP- 2-EN -1-ONE
3sza CRYSTAL STRUCTURE OF HUMAN ALDH3A1 - APO FORM