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(-) Description

Title :  CRYSTALS STRUCTURE OF ASPARTATE BETA-SEMIALDEHYDE DEHYDROGENASE FROM VIBRIO CHOLERAE WITH PRODUCT OF S-ALLYL-L-CYSTEINE SULFOXIDE
 
Authors :  A. G. Pavlovsky, X. Liu, R. E. Viola
Date :  15 Dec 10  (Deposition) - 22 Feb 12  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxydoreductase, Nadp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. G. Pavlovsky, X. Liu, C. R. Faehnle, N. Potente, R. E. Viola
Structural Characterization Of Inhibitors With Selectivity Against Members Of A Homologous Enzyme Family.
Chem. Biol. Drug Des. V. 79 128 2012
PubMed-ID: 22039970  |  Reference-DOI: 10.1111/J.1747-0285.2011.01267.X

(-) Compounds

Molecule 1 - ASPARTATE-SEMIALDEHYDE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.2.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 28A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: VC_2036
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CYS2Mod. Amino AcidCYSTEINE
3EDO2Ligand/Ion1,2-ETHANEDIOL
4SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:101 , ASN A:133 , CYS A:134 , GLU A:240 , LYS A:243 , GLN A:350 , HOH A:809BINDING SITE FOR RESIDUE CYS A 401
2AC2SOFTWAREARG A:9 , SER A:35 , THR A:36 , SER A:37 , HOH A:531 , HOH A:546BINDING SITE FOR RESIDUE SO4 A 402
3AC3SOFTWAREARG A:309 , HOH A:504 , HOH A:735 , LYS B:232BINDING SITE FOR RESIDUE ACT A 403
4AC4SOFTWAREARG B:9 , SER B:35 , THR B:36 , SER B:37 , HOH B:548 , HOH B:787BINDING SITE FOR RESIDUE SO4 B 401
5AC5SOFTWAREARG B:101 , ASN B:133 , CYS B:134 , GLU B:240 , GLN B:350 , HOH B:632 , HOH B:706BINDING SITE FOR RESIDUE CYS B 402
6AC6SOFTWAREARG B:19 , GLU B:22 , GLY B:323BINDING SITE FOR RESIDUE EDO B 403
7AC7SOFTWAREGLY B:10 , MET B:11 , GLY B:167 , ALA B:168 , HOH B:749 , HOH B:781BINDING SITE FOR RESIDUE EDO B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q0E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q0E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q0E)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ASDPS01103 Aspartate-semialdehyde dehydrogenase signature.DHAS1_VIBCH261-275
 		  2A:261-275
B:261-275

(-) Exons   (0, 0)

(no "Exon" information available for 3Q0E)

(-) 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:370
 aligned with DHAS1_VIBCH | Q9KQG2 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:371
                                                                                                                                                                                                                                                                                                                                                                                                           370 
                                    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 
          DHAS1_VIBCH     1 MRVGLVGWRGMVGSVLMQRMVEERDFDLIEPVFFSTSQIGVPAPNFGKDAGMLHDAFDIESLKQLDAVITCQGGSYTEKVYPALRQAGWKGYWIDAASTLRMDKEAIITLDPVNLKQILHGIHHGTKTFVGGNCTVSLMLMALGGLYERGLVEWMSAMTYQAASGAGAQNMRELISQMGVINDAVSSELANPASSILDIDKKVAETMRSGSFPTDNFGVPLAGSLIPWIDVKRDNGQSKEEWKAGVEANKILGLQDSPVPIDGTCVRIGAMRCHSQALTIKLKQNIPLDEIEEMIATHNDWVKVIPNERDITARELTPAKVTGTLSVPVGRLRKMAMGDDFLNAFTVGDQLLWGAAEPLRRTLRIILAEK-   -
               SCOP domains d3q0ea1 A:1-132,A:355-369 Aspartate beta-semialdehyde dehydrogenase                                                                 d3q0ea2 A:133-354 Aspartate beta-semialdehyde dehydrogenase                                                                                                                                                                   d3q0ea1        -- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhhhhhhheeeeee..................ee..hhhhhhh..eeee..hhhhhhhhhhhhhhh....eeee..........eeeehhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh............................hhhhhhhhhhhhhhh........ee..eee.....eeeeeeeeee....hhhhhhhhhhh....eee...hhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeeeeee......hhhhhhhhhhhhhh-. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASD            ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q0e A   1 MRVGLVGWRGMVGSVLMQRMVEERDFDLIEPVFFSTSQIGVPAPNFGKDAGMLHDAFDIESLKQLDAVITCQGGSYTEKVYPALRQAGWKGYWIDAASTLRMDKEAIITLDPVNLKQILHGIHHGTKTFVGGNCTVSLMLMALGGLYERGLVEWMSAMTYQAASGAGAQNMRELISQMGVINDAVSSELANPASSILDIDKKVAETMRSGSFPTDNFGVPLAGSLIPWIDVKRDNGQSKEEWKAGVEANKILGLQDSPVPIDGTCVRIGAMRCHSQALTIKLKQNIPLDEIEEMIATHNDWVKVIPNERDITARELTPAKVTGTLSVPVGRLRKMAMGDDFLNAFTVGDQLLWGAAEPLRRTLRIILAE-C 401
                                    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        |-|
                                                                                                                                                                                                                                                                                                                                                                                                          369 |
                                                                                                                                                                                                                                                                                                                                                                                                            401


Chain B from PDB  Type:PROTEIN  Length:369
 aligned with DHAS1_VIBCH | Q9KQG2 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:369
                                    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         
          DHAS1_VIBCH     1 MRVGLVGWRGMVGSVLMQRMVEERDFDLIEPVFFSTSQIGVPAPNFGKDAGMLHDAFDIESLKQLDAVITCQGGSYTEKVYPALRQAGWKGYWIDAASTLRMDKEAIITLDPVNLKQILHGIHHGTKTFVGGNCTVSLMLMALGGLYERGLVEWMSAMTYQAASGAGAQNMRELISQMGVINDAVSSELANPASSILDIDKKVAETMRSGSFPTDNFGVPLAGSLIPWIDVKRDNGQSKEEWKAGVEANKILGLQDSPVPIDGTCVRIGAMRCHSQALTIKLKQNIPLDEIEEMIATHNDWVKVIPNERDITARELTPAKVTGTLSVPVGRLRKMAMGDDFLNAFTVGDQLLWGAAEPLRRTLRIILAE 369
               SCOP domains d3q0eb1 B:1-132,B:355-369 Aspartate beta-semialdehyde dehydrogenase                                                                 d3q0eb2 B:133-354 Aspartate beta-semialdehyde dehydrogenase                                                                                                                                                                   d3q0eb1         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhhhhhhheeeeee..................ee..hhhhhh...eeee..hhhhhhhhhhhhhhh....eeee..........eeeehhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...............ee...........hhhhhhhhhhhhhhh........ee....ee....eeeeeeeeee....hhhhhhhhhhh....eee...hhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeeeeeee.....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASD            ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q0e B   1 MRVGLVGWRGMVGSVLMQRMVEERDFDLIEPVFFSTSQIGVPAPNFGKDAGMLHDAFDIESLKQLDAVITCQGGSYTEKVYPALRQAGWKGYWIDAASTLRMDKEAIITLDPVNLKQILHGIHHGTKTFVGGNCTVSLMLMALGGLYERGLVEWMSAMTYQAASGAGAQNMRELISQMGVINDAVSSELANPASSILDIDKKVAETMRSGSFPTDNFGVPLAGSLIPWIDVKRDNGQSKEEWKAGVEANKILGLQDSPVPIDGTCVRIGAMRCHSQALTIKLKQNIPLDEIEEMIATHNDWVKVIPNERDITARELTPAKVTGTLSVPVGRLRKMAMGDDFLNAFTVGDQLLWGAAEPLRRTLRIILAE 369
                                    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
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q0E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3Q0E)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DHAS1_VIBCH | Q9KQG2)
molecular function
    GO:0003942    N-acetyl-gamma-glutamyl-phosphate reductase activity    Catalysis of the reaction: N-acetyl-L-glutamate 5-semialdehyde + NADP+ + phosphate = N-acetyl-5-glutamyl phosphate + NADPH + H+.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0004073    aspartate-semialdehyde dehydrogenase activity    Catalysis of the reaction: L-aspartate 4-semialdehyde + NADP(+) + phosphate = 4-phospho-L-aspartate + H(+) + NADPH.
    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:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
biological process
    GO:0071266    'de novo' L-methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of L-methionine, the L-enantiomer of (2S)-2-amino-4-(methylsulfanyl)butanoic acid, from simpler components.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0019877    diaminopimelate biosynthetic process    The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
    GO:0009097    isoleucine biosynthetic process    The chemical reactions and pathways resulting in the formation of isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid.
    GO:0009085    lysine biosynthetic process    The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
    GO:0009089    lysine biosynthetic process via diaminopimelate    The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
    GO:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
    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:0009088    threonine biosynthetic process    The chemical reactions and pathways resulting in the formation of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DHAS1_VIBCH | Q9KQG2: 1mb4 1mc4 3pzr 4r5m

(-) Related Entries Specified in the PDB File

3pwk 3pws 3pyl 3pyx 3pzb 3pzr 3q11 3q1l