Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AMP-BOUND SACCHAROPINE DEHYDROGENASE (L-LYS FORMING) FROM SACCHAROMYCES CEREVISIAE
 
Authors :  B. Andi, H. Xu, P. F. Cook, A. H. West
Date :  28 Jul 07  (Deposition) - 30 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Amp, Rossmann Fold, Alpha-Aminoadipate Pathway, Fungal Lysine Biosynthesis, Acetylation, Amino-Acid Biosynthesis, Cytoplasm, Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Andi, H. Xu, P. F. Cook, A. H. West
Crystal Structures Of Ligand-Bound Saccharopine Dehydrogenase From Saccharomyces Cerevisiae
Biochemistry V. 46 12512 2007
PubMed-ID: 17939687  |  Reference-DOI: 10.1021/BI701428M
(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
    Expression System Plasmid: PSDHHX1 (PET16B DERIVATIVE)
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 562
    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, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:200 , LEU A:202 , GLY A:203 , ARG A:204 , CYS A:205 , ASP A:227 , ILE A:228 , THR A:231 , ILE A:250 , HOH A:507 , HOH A:607 , HOH A:684 , HOH A:746 , HOH A:753 , HOH A:797 , HOH A:803 , HOH A:840BINDING SITE FOR RESIDUE AMP A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QRK)

(-) 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 2QRK)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YIR034C1YIR034C.1IX:420733-4196121122LYS1_YEAST1-3733731A:3-367365

(-) 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:365
 aligned with LYS1_YEAST | P38998 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:365
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362     
           LYS1_YEAST     3 AVTLHLRAETKPLEARAALTPTTVKKLIAKGFKIYVEDSPQSTFNINEYRQAGAIIVPAGSWKTAPRDRIIIGLKEMPETDTFPLVHEHIQFAHCYKDQAGWQNVLMRFIKGHGTLYDLEFLENDQGRRVAAFGFYAGFAGAALGVRDWAFKQTHSDDEDLPAVSPYPNEKALVKDVTKDYKEALATGARKPTVLIIGALGRCGSGAIDLLHKVGIPDANILKWDIKETSRGGPFDEIPQADIFINCIYLSKPIAPFTNMEKLNNPNRRLRTVVDVSADTTNPHNPIPIYTVATVFNKPTVLVPTTAGPKLSVISIDHLPSLLPREASEFFSHDLLPSLELLPQRKTAPVWVRAKKLFDRHCARV 367
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----AlaDh_PNT_N-2qrkA01 A:7-142                                                                                                             --------------------------------AlaDh_PNT_C-2qrkA02 A:175-317                                                                                                                  -------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.............hhhhhhhhhhh..eeeee.......hhhhhhhhh.eee..hhhhhh....eee...............eeee.........hhhhhhhhhhhhh.eeee.hhh..........hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhh..hhh.eeeehhhhhh.....hhhhhh.eeee............hhhhhh.......eeee.........................ee.........eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-367 UniProt: 1-373 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                            Transcript 1
                 2qrk A   3 AVTLHLRAETKPLEARAALTPTTVKKLIAKGFKIYVEDSPQSTFNINEYRQAGAIIVPAGSWKTAPRDRIIIGLKEMPETDTFPLVHEHIQFAHCYKDQAGWQNVLMRFIKGHGTLYDLEFLENDQGRRVAAFGFYAGFAGAALGVRDWAFKQTHSDDEDLPAVSPYPNEKALVKDVTKDYKEALATGARKPTVLIIGALGRCGSGAIDLLHKVGIPDANILKWDIKETSRGGPFDEIPQADIFINCIYLSKPIAPFTNMEKLNNPNRRLRTVVDVSADTTNPHNPIPIYTVATVFNKPTVLVPTTAGPKLSVISIDHLPSLLPREASEFFSHDLLPSLELLPQRKTAPVWVRAKKLFDRHCARV 367
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
   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 2QRK)

(-) CATH Domains  (0, 0)

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

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    AMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:235 - Pro A:236   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2qrk
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  LYS1_YEAST | P38998
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.5.1.7
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  LYS1_YEAST | P38998
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LYS1_YEAST | P38998: 2q99 2qrj 2qrl 3ugk 3uh1 3uha

(-) Related Entries Specified in the PDB File

2q99 THE SAME PROTEIN IN APO FORM.