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(-) Description

Title :  RECOMBINANT YEAST FUMARASE
 
Authors :  T. M. Weaver, M. R. Lees, L. J. Banaszak
Date :  07 Jan 98  (Deposition) - 08 Jul 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Lyase, Fumarase, Krebs Cycle, Active Site Water, Hydratase, Multi- Subunit Active Site (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Weaver, M. Lees, V. Zaitsev, I. Zaitseva, E. Duke, P. Lindley, S. Mcsweeny, A. Svensson, J. Keruchenko, I. Keruchenko, K. Gladilin, L. Banaszak
Crystal Structures Of Native And Recombinant Yeast Fumarase
J. Mol. Biol. V. 280 431 1998
PubMed-ID: 9665847  |  Reference-DOI: 10.1006/JMBI.1998.1862

(-) Compounds

Molecule 1 - FUMARASE
    ChainsA
    EC Number4.2.1.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cellular LocationCYTOPLASM
    Expression System GeneFUM1
    Expression System PlasmidPASKYMFUM
    Expression System StrainJM109
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneFUM1
    MutationYES
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymYFUM

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1YFM)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AVEAUTHORHIS A:213AUTHOR STATED THIS AS MULTI-SUBUNIT ACTIVE SITE OF FUMARASE, WITH H213, T126, S124, AND N166 ALL PROVIDING HYDROGEN BONDS TO THE PUTATIVE CATALYTIC WATER MOLECULE.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:326 -Pro A:327

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FUMARATE_LYASESPS00163 Fumarate lyases signature.FUMH_YEAST342-351  1A:342-351
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FUMARATE_LYASESPS00163 Fumarate lyases signature.FUMH_YEAST342-351  4A:342-351

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPL262W1YPL262W.1XVI:47336-488021467FUMH_YEAST1-4884881A:27-485 (gaps)459

(-) 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:450
 aligned with FUMH_YEAST | P08417 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:459
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476         
           FUMH_YEAST    27 SFRTETDAFGEIHVPADKYWGAQTQRSFQNFKIGGARERMPLPLVHAFGVLKKSAAIVNESLGGLDPKISKAIQQAADEVASGKLDDHFPLVVFQTGSGTQSNMNANEVISNRAIEILGGKIGSKQVHPNNHCNQSQSSNDTFPTVMHIAASLQIQNELIPELTNLKNALEAKSKEFDHIVKIGRTHLQDATPLTLGQEFSGYVQQVENGIQRVAHSLKTLSFLAQGGTAVGTGLNTKPGFDVKIAEQISKETGLKFQTAPNKFEALAAHDAIVECSGALNTLACSLFKIAQDIRYLGSGPRCGYHELMLPENEPGSSIMPGKVNPTQNEALTQVCVQVMGNNAAITFAGSQGQFELNVFKPVMIANLLNSIRLITDAAYSFRVHCVEGIKANEPRIHELLTKSLMLVTALNPKIGYDAASKVAKNAHKKGITLKESALELGVLTEKEFDEWVVPEHML 485
               SCOP domains d1yfma_ A: Fumarase                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains --1yfmA01 A:29-163 Fumarase/aspartase (N-terminal domain)                                                                                1yfmA02 A:164-432 Fumarase/aspartase (Central domain)                                                                                                                                                                                                                        1yfmA03 A:433-484                                   - CATH domains
               Pfam domains ---------Lyase_1-1yfmA02 A:36-367                                                                                                                                                                                                                                                                                                                    -----------------------------------------------------------------FumaraseC_C-1yfmA01 A:433-485                         Pfam domains
         Sec.struct. author .eeee......eeee......hhhhhhh......hhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhh...........hhhhhhhhhhhhhhhhh.---------..hhhh......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....eee..hhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhh.........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.............................hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh..hhh...hhh..hhhhhhhhhhhhhh...hhhhhhh.....hhhhhhh..hhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FUMARATE_L-------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:27-485 (gaps) UniProt: 1-488 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                  Transcript 1
                 1yfm A  27 SFRTETDAFGEIHVPADKYWGAQTQRSFQNFKIGGARERMPLPLVHAFGVLKKSAAIVNESLGGLDPKISKAIQQAADEVASGKLDDHFPLVVFQTGSGTQSNMNANEVISNRAIEI---------VHPNNHCNQSQSSNDTFPTVMHIAASLQIQNELIPELTNLKNALEAKSKEFDHIVKIGRTHLQDATPLTLGQEFSGYVQQVENGIQRVAHSLKTLSFLAQGGTAVGTGLNTKPGFDVKIAEQISKETGLKFQTAPNRFEALAAHDAIVECSGALNTLACSLFKIAQDIRYLGSGPRCGYHELMLPENEPGSSIMPGKVNPTQNEALTQVCVQVMGNNAAITFAGSQGQFELNVFKPVMIANLLNSIRLITDAAYSFRVHCVEGIKANEPRIHELLTKSLMLVTALNPKIGYDAASKVAKNAHKKGITLKESALELGVLTEKEFDEWVVPEHML 485
                                    36        46        56        66        76        86        96       106       116       126       136      |  -      |156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476         
                                                                                                                                              143       153                                                                                                                                                                                                                                                                                                                                            

   Legend:   → Mismatch (orange background)
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  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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (3, 3)

Asymmetric Unit

(-) Pfam Domains  (2, 2)

Asymmetric Unit

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (FUMH_YEAST | P08417)
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:0004333    fumarate hydratase activity    Catalysis of the reaction: (S)-malate = fumarate + H(2)O.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0006106    fumarate metabolic process    The chemical reactions and pathways involving fumarate, the anion of trans-1,2-ethenedicarboxylic acid, the diastereoisomer of maleate. It is a key intermediate in metabolism and is formed in the TCA cycle from succinate and converted into malate.
    GO:0006108    malate metabolic process    The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
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:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0045239    tricarboxylic acid cycle enzyme complex    Any of the heteromeric enzymes that act in the TCA cycle.

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