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(-) Description

Title :  CRYSTAL STRUCTURE OF SACCHAROPINE DEHYDROGENASE FROM SACCHAROMYCES CERVISIAE COMPLEXED WITH NAD.
 
Authors :  P. F. Cook, V. P. Kumar, L. M. Thomas, A. H. West, K. D. Bobyk
Date :  03 Nov 11  (Deposition) - 01 Feb 12  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Lysine Biosynthesis, Proton Shuttle, Enzyme Mechanism, Nad Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. P. Kumar, L. M. Thomas, K. D. Bobyk, B. Andi, P. F. Cook, A. H. West
Evidence In Support Of Lysine 77 And Histidine 96 As Acid-Base Catalytic Residues In Saccharopine Dehydrogenase From Saccharomyces Cerevisiae.
Biochemistry V. 51 857 2012
PubMed-ID: 22243403  |  Reference-DOI: 10.1021/BI201808U

(-) Compounds

Molecule 1 - SACCHAROPINE DEHYDROGENASE [NAD+, L-LYSINE-FORMING]
    Chains: A, B
    EC Number: 1.5.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-16B
    Expression System Taxid: 562
    Gene: LYS1, YIR034C
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: SDH, LYSINE--2-OXOGLUTARATE REDUCTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): AB
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:130 , ALA A:139 , ILE A:199 , GLY A:200 , GLY A:203 , ARG A:204 , SER A:205 , ASP A:227 , ILE A:228 , THR A:231 , ILE A:250 , TYR A:251 , ILE A:256 , VAL A:278 , ILE A:318 , ASP A:319 , HIS A:320 , LEU A:321 , PRO A:322BINDING SITE FOR RESIDUE NAD A 374
2AC2SOFTWAREARG B:130 , ALA B:139 , ILE B:199 , GLY B:200 , GLY B:203 , ARG B:204 , SER B:205 , ASP B:227 , ILE B:228 , THR B:231 , CYS B:249 , ILE B:250 , TYR B:251 , ILE B:256 , VAL B:278 , ILE B:318 , ASP B:319 , HIS B:320 , LEU B:321 , PRO B:322 , HOH B:377BINDING SITE FOR RESIDUE NAD B 374
3AC3SOFTWARELYS A:193 , LYS B:193BINDING SITE FOR RESIDUE CL A 375

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:235 -Pro A:236
2Gly B:235 -Pro B:236

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YIR034C1YIR034C.1IX:420733-4196121122LYS1_YEAST1-3733732A:3-367
B:3-367		365
365

(-) Sequences/Alignments

Asymmetric 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 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.............hhhhhhhhhhh..eeeee.......hhhhhhhh..eee..hhhhhh....eee...............eeee.........hhhhhhhhhhh...eeee.hhh..........hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhhhhh.hhh.eeeehhhhhh.....hhhhhh.eeee............hhhhhh.......eeee.........................eee.......eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-367 UniProt: 1-373 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                            Transcript 1
                 3uha A   3 AVTLHLRAETKPLEARAALTPTTVKKLIAKGFKIYVEDSPQSTFNINEYRQAGAIIVPAGSWKTAPRDRIIIGLKEMPETDTFPLVHEHIQFAHCYKDQAGWQNVLMRFIKGHGTLYDLEFLENDQGRRVAAFGFYAGFAGAALGVRDWAFKQTHSDDEDLPAVSPYPNEKALVKDVTKDYKEALATGARKPTVLIIGALGRSGSGAIDLLHKVGIPDANILKWDIKETSRGGPFDEIPQADIFINCIYLSKPIAPFTNMEKLNNPNRRLRTVVDVSADTTNPHNPIPIYTVATVFNKPTVLVPTTAGPKLSVISIDHLPSLLPREASEFFSHDLLPSLELLPQRKTAPVWVRAKKLFDRHCARV 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     


Chain B 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 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.............hhhhhhhhhhh..eeeee.......hhhhhhhh..eee..hhhhh.....eee...............eeee.........hhhhhhhhhhhhh.eeee.hhh..........hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhhhh..hhh.eeeehhhhhh.....hhhhhh.eeee............hhhhhh.......eeee.........................eee.......eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-367 UniProt: 1-373 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                            Transcript 1
                 3uha B   3 AVTLHLRAETKPLEARAALTPTTVKKLIAKGFKIYVEDSPQSTFNINEYRQAGAIIVPAGSWKTAPRDRIIIGLKEMPETDTFPLVHEHIQFAHCYKDQAGWQNVLMRFIKGHGTLYDLEFLENDQGRRVAAFGFYAGFAGAALGVRDWAFKQTHSDDEDLPAVSPYPNEKALVKDVTKDYKEALATGARKPTVLIIGALGRSGSGAIDLLHKVGIPDANILKWDIKETSRGGPFDEIPQADIFINCIYLSKPIAPFTNMEKLNNPNRRLRTVVDVSADTTNPHNPIPIYTVATVFNKPTVLVPTTAGPKLSVISIDHLPSLLPREASEFFSHDLLPSLELLPQRKTAPVWVRAKKLFDRHCARV 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 3UHA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  3uha
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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: 2q99 2qrj 2qrk 2qrl 3ugk 3uh1

(-) Related Entries Specified in the PDB File

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