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(-) Description

Title :  CRYSTAL STRUCTURE OF SACCHAROPINE DEHYDROGENASE FROM SACCHAROMYCES CEREVISIAE
 
Authors :  A. M. Berghuis, D. L. Burk
Date :  12 Jun 07  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym./Biol. Unit :  A
Keywords :  Dehydrogenase, Alpha-Aminoadipate Pathway, Fungal Lysine Synthesis, Alpha/Beta Protein, Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. L. Burk, J. Hwang, E. Kwok, L. Marrone, V. Goodfellow, G. I. Dmitrienko, A. M. Berghuis
Structural Studies Of The Final Enzyme In The Alpha-Aminoadipate Pathway-Saccharopine Dehydrogenase From Saccharomyces Cerevisiae
J. Mol. Biol. V. 373 745 2007
PubMed-ID: 17854830  |  Reference-DOI: 10.1016/J.JMB.2007.08.044
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SACCHAROPINE DEHYDROGENASE [NAD+, L-LYSINE- FORMING
    Chains: A
    EC Number: 1.5.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PGEX-6T-3
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: LYS1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: LYSINE--2-OXOGLUTARATE REDUCTASE, SDH

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2Q99)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:205 -A:249

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:235 -Pro A:236

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q99)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q99)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YIR034C1YIR034C.1IX:420733-4196121122LYS1_YEAST1-3733731A:2-373372

(-) 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:372
 aligned with LYS1_YEAST | P38998 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:372
                                    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  
           LYS1_YEAST     2 AAVTLHLRAETKPLEARAALTPTTVKKLIAKGFKIYVEDSPQSTFNINEYRQAGAIIVPAGSWKTAPRDRIIIGLKEMPETDTFPLVHEHIQFAHCYKDQAGWQNVLMRFIKGHGTLYDLEFLENDQGRRVAAFGFYAGFAGAALGVRDWAFKQTHSDDEDLPAVSPYPNEKALVKDVTKDYKEALATGARKPTVLIIGALGRCGSGAIDLLHKVGIPDANILKWDIKETSRGGPFDEIPQADIFINCIYLSKPIAPFTNMEKLNNPNRRLRTVVDVSADTTNPHNPIPIYTVATVFNKPTVLVPTTAGPKLSVISIDHLPSLLPREASEFFSHDLLPSLELLPQRKTAPVWVRAKKLFDRHCARVKRSSRL 373
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----AlaDh_PNT_N-2q99A01 A:7-142                                                                                                             --------------------------------AlaDh_PNT_C-2q99A02 A:175-317                                                                                                                  -------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.............hhhhhhhhhhh..eeeee.......hhhhhhhh..eee..hhhhhh....eee...............eeee.........hhhhhhhhhhhhh.eeee.hhh..........hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhh.hhh.eeeehhhhhh.....hhhhhh.eeee............hhhhhh.......eeee.........................ee.........eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-373 UniProt: 1-373 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                   Transcript 1
                 2q99 A   2 AAVTLHLRAETKPLEARAALTPTTVKKLIAKGFKIYVEDSPQSTFNINEYRQAGAIIVPAGSWKTAPRDRIIIGLKEmPETDTFPLVHEHIQFAHCYKDQAGWQNVLmRFIKGHGTLYDLEFLENDQGRRVAAFGFYAGFAGAALGVRDWAFKQTHSDDEDLPAVSPYPNEKALVKDVTKDYKEALATGARKPTVLIIGALGRCGSGAIDLLHKVGIPDANILKWDIKETSRGGPFDEIPQADIFINCIYLSKPIAPFTNmEKLNNPNRRLRTVVDVSADTTNPHNPIPIYTVATVFNKPTVLVPTTAGPKLSVISIDHLPSLLPREASEFFSHDLLPSLELLPQRKTAPVWVRAKKLFDRHCARVKRSSRL 373
                                    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  
                                                                                                        79-MSE                       109-MSE                                                                                                                                                  262-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 2Q99)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q99)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Form_Glyc_dh (56)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LYS1_YEAST | P38998)
molecular function
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    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: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).
    GO:0004754    saccharopine dehydrogenase (NAD+, L-lysine-forming) activity    Catalysis of the reaction: L-saccharopine + H(2)O + NAD(+) = 2-oxoglutarate + L-lysine + H(+) + NADH.
biological process
    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:0009085    lysine biosynthetic process    The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
    GO:0019878    lysine biosynthetic process via aminoadipic acid    The chemical reactions and pathways resulting in the formation of lysine by the aminoadipic pathway.
    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.
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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  Cis Peptide Bonds
    Gly A:235 - Pro A:236   [ RasMol ]  
 

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  2q99
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  LYS1_YEAST | P38998
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  1.5.1.7
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 Related Entries

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

UniProtKB/Swiss-Prot
        LYS1_YEAST | P38998: 2qrj 2qrk 2qrl 3ugk 3uh1 3uha

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Q99)