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(-) Description

Title :  CRYSTAL STRUCTURE OF APO FUMARASE C FROM ESCHERICHIA COLI
 
Authors :  T. Weaver
Date :  31 Dec 04  (Deposition) - 18 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Fumarase, Kreb'S Cycle, Apo, Allosteric, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Weaver
Structure Of Free Fumarase C From Escherichia Coli.
Acta Crystallogr. , Sect. D V. 61 1395 2005
PubMed-ID: 16204892  |  Reference-DOI: 10.1107/S0907444905024194

(-) Compounds

Molecule 1 - FUMARATE HYDRATASE CLASS II
    ChainsA
    EC Number4.2.1.2
    FragmentA-SUBUNIT
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12
    SynonymFUMARASE C

 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 1YFE)

(-) Sites  (0, 0)

(no "Site" information available for 1YFE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:301 -Pro A:302

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FUMARATE_LYASESPS00163 Fumarate lyases signature.FUMC_ECOLI317-326  1A:317-326
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FUMARATE_LYASESPS00163 Fumarate lyases signature.FUMC_ECOLI317-326  4A:317-326

(-) Exons   (0, 0)

(no "Exon" information available for 1YFE)

(-) 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:457
 aligned with FUMC_ECOLI | P05042 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:457
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       
           FUMC_ECOLI     4 VRSEKDSMGAIDVPADKLWGAQTQRSLEHFRISTEKMPTSLIHALALTKRAAAKVNEDLGLLSEEKASAIRQAADEVLAGQHDDEFPLAIWQTGSGTQSNMNMNEVLANRASELLGGVRGMERKVHPNDDVNKSQSSNDVFPTAMHVAALLALRKQLIPQLKTLTQTLNEKSRAFADIVKIGRTHLQDATPLTLGQEISGWVAMLEHNLKHIEYSLPHVAELALGGTAVGTGLNTHPEYARRVADELAVITCAPFVTAPNKFEALATCDALVQAHGALKGLAASLMKIANDVRWLASGPRCGIGEISIPENEPGSSIMPGKVNPTQCEALTMLCCQVMGNDVAINMGGASGNFELNVFRPMVIHNFLQSVRLLADGMESFNKHCAVGIEPNRERINQLLNESLMLVTALNTHIGYDKAAEIAKKAHKEGLTLKAAALALGYLSEAEFDSWVRPEQMV 460
               SCOP domains d1yfea_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1yfeA01 A:4-138 Fumarase/aspartase (N-terminal domain)                                                                                 1yfeA02 A:139-407 Fumarase/aspartase (Central domain)                                                                                                                                                                                                                        1yfeA03 A:408-460                                     CATH domains
               Pfam domains --------Lyase_1-1yfeA02 A:12-342                                                                                                                                                                                                                                                                                                                   -----------------------------------------------------------------FumaraseC_C-1yfeA01 A:408-460                         Pfam domains
         Sec.struct. author .eeeee..eeeee......hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhee...............hhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee................hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhh..hhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FUMARATE_L-------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yfe A   4 VRSEKDSMGAIDVPADKLWGAQTQRSLEHFRISTEKMPTSLIHALALTKRAAAKVNEDLGLLSEEKASAIRQAADEVLAGQHDDEFPLAIWQTGSGTQSNMNMNEVLANRASELLGGVRGMERKVHPNDDVNKSQSSNDVFPTAMHVAALLALRKQLIPQLKTLTQTLNEKSRAFADIVKIGRTHLQDATPLTLGQEISGWVAMLEHNLKHIEYSLPHVAELALGGTAVGTGLNTHPEYARRVADELAVITCAPFVTAPNKFEALATCDALVQAHGALKGLAASLMKIANDVRWLASGPRCGIGEISIPENEPGSSIMPGKVNPTQCEALTMLCCQVMGNDVAINMGGASGNFELNVFRPMVIHNFLQSVRLLADGMESFNKHCAVGIEPNRERINQLLNESLMLVTALNTHIGYDKAAEIAKKAHKEGLTLKAAALALGYLSEAEFDSWVRPEQMV 460
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       

   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  (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   (FUMC_ECOLI | P05042)
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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    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:0045239    tricarboxylic acid cycle enzyme complex    Any of the heteromeric enzymes that act in the TCA cycle.

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    Gly A:301 - Pro A:302   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        FUMC_ECOLI | P050421fuo 1fup 1fuq 1fur 1kq7 2fus

(-) Related Entries Specified in the PDB File

1fuo BOUND TO CITRATE
1fup BOUND TO PYROMELLITIC ACID
1fuq BOUND TO 3-TRIMETHYLSILYLSUCCINIC ACID