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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NAD-DEPENDENT 5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH NAD
 
Authors :  A. F. Monzingo, A. Breksa, S. Ernst, D. R. Appling, J. D. Robertus
Date :  31 Jan 00  (Deposition) - 06 Dec 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Nucleotide-Binding Domain, Protein-Nad Complex, Monofunctional, Dehydrogenase, Folate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. F. Monzingo, A. Breksa, S. Ernst, D. R. Appling, J. D. Robertus
The X-Ray Structure Of The Nad-Dependent 5, 10-Methylenetetrahydrofolate Dehydrogenase From Saccharomyces Cerevisiae.
Protein Sci. V. 9 1374 2000
PubMed-ID: 10933503
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE
    ChainsA
    EC Number1.5.1.15
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:184 , ARG A:185 , SER A:186 , VAL A:189 , VAL A:207 , ASP A:208 , VAL A:209 , GLY A:252 , VAL A:253 , PRO A:254 , PHE A:274 , CYS A:276 , THR A:295 , HOH A:322 , HOH A:326 , HOH A:327BINDING SITE FOR RESIDUE NAD A 321

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EE9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:99 -Pro A:100

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EE9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EE9)

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YKR080W1YKR080W.1XI:590037-590999963MTD1_YEAST1-3203201A:3-319317

(-) 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:317
 aligned with MTD1_YEAST | Q02046 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:317
                                    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       
           MTD1_YEAST     3 KPGRTILASKVAETFNTEIINNVEEYKKTHNGQGPLLVGFLANNDPAAKMYATWTQKTSESMGFRYDLRVIEDKDFLEEAIIQANGDDSVNGIMVYFPVFGNAQDQYLQQVVCKEKDVEGLNHVYYQNLYHNVRYLDKENRLKSILPCTPLAIVKILEFLKIYNNLLPEGNRLYGKKCIVINRSEIVGRPLAALLANDGATVYSVDVNNIQKFTRGESLKLNKHHVEDLGEYSEDLLKKCSLDSDVVITGVPSENYKFPTEYIKEGAVCINFACTKNFSDDVKEKASLYVPMTGKVTIAMLLRNMLRLVRNVELSKE 319
               SCOP domains d1ee9a2 A:3-148 Tetrahydrofolate dehydrogenase/cyclohydrolase                                                                                     d1ee9a1 A:149-319 Methylenetetrahydrofolate dehydrogenase/cyclohydrolase                                                                                                    SCOP domains
               CATH domains 1ee9A01 --1ee9A02 A:13-120,A:297-319 Leucine Dehydrogenase, chain A, domain 1                                         ----------------------------1ee9A01 A:3-10,A:149-296 NAD(P)-binding Rossmann-like Domain                                                                                        1ee9A02                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeehhhhhhh.hhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhh.....eeeee.....hhhhhhhhhh...........hhhhhhhhh...............hhhhhhhhhhhhhh................eeeee.....hhhhhhhhhhh...eeeee....eeeee..........eeeeee...hhhhhhhhhh.eeeee..................eeeee.............eeeee...hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-319 UniProt: 1-320 [INCOMPLETE]                                                                                                                                                                                                                                                                            Transcript 1
                 1ee9 A   3 KPGRTILASKVAETFNTEIINNVEEYKKTHNGQGPLLVGFLANNDPAAKMYATWTQKTSESMGFRYDLRVIEDKDFLEEAIIQANGDDSVNGIMVYFPVFGNAQDQYLQQVVCKEKDVEGLNHVYYQNLYHNVRYLDKENRLKSILPCTPLAIVKILEFLKIYNNLLPEGNRLYGKKCIVINRSEIVGRPLAALLANDGATVYSVDVNNIQKFTRGESLKLNKHHVEDLGEYSEDLLKKCSLDSDVVITGVPSENYKFPTEYIKEGAVCINFACTKNFSDDVKEKASLYVPMTGKVTIAMLLRNMLRLVRNVELSKE 319
                                    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       

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EE9)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (MTD1_YEAST | Q02046)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004477    methenyltetrahydrofolate cyclohydrolase activity    Catalysis of the reaction: 5,10-methenyltetrahydrofolate + H2O = 10-formyltetrahydrofolate.
    GO:0004487    methylenetetrahydrofolate dehydrogenase (NAD+) activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + NAD(+) = 5,10-methenyltetrahydrofolate + NADH.
    GO:0004488    methylenetetrahydrofolate dehydrogenase (NADP+) activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + 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.
biological process
    GO:0009396    folic acid-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of folic acid and its derivatives.
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    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:0009113    purine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
    GO:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MTD1_YEAST | Q020461edz

(-) Related Entries Specified in the PDB File

1edz 1EDZ CONTAINS THE SAME PROTEIN WITHOUT NAD BOUND