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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF RAT LIVER THREONINE DEAMINASE
 
Authors :  M. Scarselli, G. Padula, A. Bernini, O. Spiga, A. Ciutti, N. Niccolai
Date :  10 Dec 03  (Deposition) - 13 Jan 04  (Release) - 13 Jan 04  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,_#
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Aminotransferase, Protein Modelling, Pyridoxal-Phosphate, Threonine Deaminase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Scarselli, M. G. Padula, A. Bernini, O. Spiga, A. Ciutti, R. Leoncini, D. Vannoni, E. Marinello, N. Niccolai
Structure And Function Correlations Between The Rat Liver Threonine Deaminase And Aminotransferases
Biochim. Biophys. Acta V. 1645 40 2003
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-SERINE DEHYDRATASE/L-THREONINE DEAMINASE
    Chains: A
    EC Number: 4.3.1.19
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Strain: WISTAR
    Synonym: L-SERINE DEHYDRATASE, L-SERINE DEAMINASE, SDH, L- THREONINE DEHYDRATASE, L-THREONINE DEAMINASE, TDH
    Tissue: LIVER

 Structural Features

(-) Chains, Units

  
Theoretical Model : 
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

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

Theoretical Model (1, 1)
No.NameCountTypeFull Name
1PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1RSQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Ser A:149 -Ala A:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDRATASE_SER_THRPS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site.SDHL_RAT32-45  1A:24-37

(-) Exons   (0, 0)

(no "Exon" information available for 1RSQ)

(-) Sequences/Alignments

Theoretical Model
   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:319
 aligned with SDHL_RAT | P09367 from UniProtKB/Swiss-Prot  Length:363

    Alignment length:355
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358     
             SDHL_RAT     9 VKTPLRDSMALSKVAGTSVFLKMDSSQPSGSFKIRGIGHLCKMKAKQGCKHFVCSSVVQIWGSRMRGRSHSGDEQPHVRSQALLPDTPSPLTAGNAGMATAYAARRLGLPATIVVPSTTPALTIERLKNEGATVEVVGEMLDEAIQLAKALEKNNPGWVYISPFDDPLIWEGHTSLVKELKETLSAKPGAIVLSVGGGGLLCGVVQGLREVGWEDVPIIAMETFGAHSFHAAVKEGKLVTLPKITSVAKALGVNTVGAQTLKLFYEHPIFSEVISDQEAVTAIEKFVDDEKILVEPACGAALAAVYSGVVCRLQAEGRLQTPLASLVVIVCGGSNISLAQLQALKAQLGLNELLK 363
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeehhhhhhhh..eeeee.hhhh.....hhhhhh.hhhhh........eeee------------------------------------..hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh.eee.....hhhhhhhhhhhhhhh...ee.....hhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhh.......eeeee...hhhhhhhhhh.....................hhhhhhhhhhh.eeeeehhhhhh.hhhhhh..............eeee..........hhhhhhh............hhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------DEHYDRATASE_SE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rsq A   1 VKTTLRDSMALSKVAGTSVFLKMDSSQPSGSFKIRGIGHLCKMKAKQGCKHFVCS------------------------------------SAGNAGMATAYAARRLGLPATIVVPSTTPALTIERLKNEGATVEVVGEMLDEAIQLAKALEKNNPGWVYISPFDDPLIWEGHTSLVKELKETLSAKPGAIVLSVGGGGLLCGVVQGLREVGWEDVPIIAMETFGAHSFHAAVKEGKLVTLPKITSVAKALGVNTVGAQTLKLFYEHTIFSEVISDQEAVTAIEKFVDDEKILVEPACGAALAAVYSGVVCRLQAEGRLQTPLASLVVIVCGGSNISLAQLQALKAQLGLNELLK 319
                                    10        20        30        40        50    |    -         -         -         - |      64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314     
                                                                                 55                                   56
   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 1RSQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1RSQ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Theoretical Model(hide GO term definitions)
Chain A   (SDHL_RAT | P09367)
molecular function
    GO:0003941    L-serine ammonia-lyase activity    Catalysis of the reaction: L-serine = pyruvate + NH3.
    GO:0004794    L-threonine ammonia-lyase activity    Catalysis of the reaction: L-threonine = 2-oxobutanoate + NH3.
    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.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0043200    response to amino acid    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 an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
    GO:0033590    response to cobalamin    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 a cobalamin (vitamin B12) stimulus.
    GO:0031667    response to nutrient levels    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 a stimulus reflecting the presence, absence, or concentration of nutrients.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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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  Cis Peptide Bonds
    Ser A:149 - Ala A:150   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        SDHL_RAT | P09367: 1pwe 1pwh

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RSQ)