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Structure of human thymidylate synthase at high salt conditions
Biology and Chemistry Report
4GYH
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE
    Text Methyl transferase, TRANSFERASE

    Polymeric Molecules

    Chain A
    Description Thymidylate synthase 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 36454.0 
    Source Method genetically manipulated  
    Entity Name TS, TSase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    SO4  SULFATE ION  O4 S   96.06  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A TYSY_HUMAN P04818     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    2.1.1.45      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    82   G1/s Transition of Mitotic Cell Cycle  The Mitotic Cell Cycle Transition by Which a Cell in G1 Commits to S Phase. the Process Begins with the Build Up of G1 Cyclin Dependent Kinase (g1 Cdk) Resulting in the Activation of Transcription of G1 Cyclins. the Process Ends with the Positive Feedback of the G1 Cyclins On the G1 Cdk Which Commits the Cell to S Phase in Which DNA Replication Is Initiated. 
    83   Regulation of Transcription Involved in G1/s Transition of Mitotic Cell Cycle  Any Process That Regulates Transcription Such That the Target Genes Are Involved in the Transition Between G1 and S Phase of the Mitotic Cell Cycle. 
    278   Mitotic Cell Cycle  Progression Through the Phases of the Mitotic Cell Cycle the Most Common Eukaryotic Cell Cycle Which Canonically Comprises Four Successive Phases Called G1 S G2 and M and Includes Replication of the Genome and the Subsequent Segregation of Chromosomes Into Daughter Cells. in Some Variant Cell Cycles Nuclear Replication or Nuclear Division May Not Be Followed by Cell Division or G1 and G2 Phases May Be Absent. 
    5976   Polysaccharide Metabolic Process  The Chemical Reactions and Pathways Involving a Polysaccharide a Polymer of Many (typically More Than 10) Monosaccharide Residues Linked Glycosidically. 
    6139   Nucleobase Containing Compound Metabolic Process  Any Cellular Metabolic Process Involving Nucleobases Nucleosides Nucleotides and Nucleic Acids. 
    6206   Pyrimidine Nucleobase Metabolic Process  The Chemical Reactions and Pathways Involving Pyrimidine Nucleobases 1 3 Diazine Organic Nitrogenous Bases. 
    6231   Dtmp Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Dtmp Deoxyribosylthymine Monophosphate (2' Deoxyribosylthymine 5' Phosphate). 
    6235   Dttp Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Dttp Deoxyribosylthymine Triphosphate. 
    7568   Aging  A Developmental Process That Is a Deterioration and Loss of Function Over Time. Aging Includes Loss of Functions Such As Resistance to Disease Homeostasis and Fertility As Well As Wear and Tear. Aging Includes Cellular Senescence But Is More Inclusive. May Precede Death (go:0016265) and May Succeed Developmental Maturation (go:0021700). 
    7623   Circadian Rhythm  Any Biological Process in an Organism That Recurs with a Regularity of Approximately 24 Hours. 
    9157   Deoxyribonucleoside Monophosphate Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of a Deoxyribonucleoside Monophosphate a Compound Consisting of a Nucleobase Linked to a Deoxyribose Sugar Esterified with Phosphate On the Sugar. 
    9165   Nucleotide Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Nucleotides Any Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Glycose Moiety; May Be Mono Di or Triphosphate; This Definition Includes Cyclic Nucleotides (nucleoside Cyclic Phosphates). 
    9636   Response to Toxic Substance  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 Toxic Stimulus. 
    14070   Response to Organic Cyclic Compound  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 Organic Cyclic Compound Stimulus. 
    19088   Immortalization of Host Cell by Virus  A Virus Induced Cellular Transformation Arising in Immortalized Cells or Cells Capable of Indefinite Replication Due to Their Ability to Produce Their Own Telomerase. 
    19860   Uracil Metabolic Process  The Chemical Reactions and Pathways Involving Uracil 2 4 Dioxopyrimidine One of the Pyrimidine Bases Occurring in RNA But Not in Dna. 
    31100   Organ Regeneration  The Regrowth of a Lost or Destroyed Organ. 
    32259   Methylation  The Process in Which a Methyl Group Is Covalently Attached to a Molecule. 
    32570   Response to Progesterone  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 Progesterone Stimulus. 
    33189   Response to Vitamin a  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 Vitamin a Stimulus. 
    34097   Response to Cytokine  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 Cytokine Stimulus. 
    42493   Response to Drug  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 Drug Stimulus. a Drug Is a Substance Used in the Diagnosis Treatment or Prevention of a Disease. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    45471   Response to Ethanol  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 Ethanol Stimulus. 
    46078   Dump Metabolic Process  The Chemical Reactions and Pathways Involving Dump Deoxyuridine (5' )monophosphate (2' Deoxyuridine 5' Phosphate). 
    46134   Pyrimidine Nucleoside Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of One of a Family of Organic Molecules Consisting of a Pyrimidine Base Covalently Bonded to a Sugar Ribose (a Ribonucleoside) or Deoxyribose (a Deoxyribonucleoside). 
    46653   Tetrahydrofolate Metabolic Process  The Chemical Reactions and Pathways Involving Tetrahydrofolate 5 6 7 8 Tetrahydrofolic Acid a Folate Derivative Bearing Additional Hydrogens On the Pterin Group. 
    46683   Response to Organophosphorus  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 Organophosphorus Stimulus. Organophosphorus Is a Compound Containing Phosphorus Bound to an Organic Molecule; Several Organophosphorus Compounds Are Used As Insecticides and They Are Highly Toxic Cholinesterase Inhibitors. 
    48589   Developmental Growth  The Increase in Size or Mass of an Entire Organism a Part of an Organism or a Cell Where the Increase in Size or Mass Has the Specific Outcome of the Progression of the Organism Over Time From One Condition to Another. 
    51216   Cartilage Development  The Process Whose Specific Outcome Is the Progression of a Cartilage Element Over Time From Its Formation to the Mature Structure. Cartilage Elements Are Skeletal Elements That Consist of Connective Tissue Dominated by Extracellular Matrix Containing Collagen Type Ii and Large Amounts of Proteoglycan Particularly Chondroitin Sulfate. 
    51384   Response to Glucocorticoid  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 Glucocorticoid Stimulus. Glucocorticoids Are Hormonal C21 Corticosteroids Synthesized From Cholesterol with the Ability to Bind with the Cortisol Receptor and Trigger Similar Effects. Glucocorticoids Act Primarily On Carbohydrate and Protein Metabolism and Have Anti Inflammatory Effects. 
    51593   Response to Folic 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 a Folic Acid Stimulus. 
    55086   Nucleobase Containing Small Molecule Metabolic Process  The Cellular Chemical Reactions and Pathways Involving a Nucleobase Containing Small Molecule: a Nucleobase a Nucleoside or a Nucleotide. 
    60574   Intestinal Epithelial Cell Maturation  The Developmental Process Independent of Morphogenetic (shape) Change That Is Required For a Columna/cuboidal Epithelial Cell of the Intestine to Attain Its Fully Functional State. a Columnar/cuboidal Epithelial Cell of the Intestine Mature As They Migrate From the Intestinal Crypt to the Villus. 
    5634   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. 
    5654   Nucleoplasm  That Part of the Nuclear Content Other Than the Chromosomes or the Nucleolus. 
    5730   Nucleolus  A Small Dense Body One or More of Which Are Present in the Nucleus of Eukaryotic Cells. It Is Rich in RNA and Protein Is Not Bounded by a Limiting Membrane and Is Not Seen During Mitosis. Its Prime Function Is the Transcription of the Nucleolar DNA Into 45s Ribosomal Precursor RNA the Processing of This RNA Into 5.8s 18s and 28s Components of Ribosomal RNA and the Association of These Components with 5s RNA and Proteins Synthesized Outside the Nucleolus. This Association Results in the Formation of Ribonucleoprotein Precursors; These Pass Into the Cytoplasm and Mature Into the 40s and 60s Subunits of the Ribosome. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5739   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. 
    5743   Mitochondrial Inner Membrane  The Inner I.e. Lumen Facing Lipid Bilayer of the Mitochondrial Envelope. It Is Highly Folded to Form Cristae. 
    5759   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. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    166   Nucleotide Binding  Interacting Selectively and Non Covalently with a Nucleotide Any Compound Consisting of a Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Ribose or Deoxyribose. 
    3729   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. 
    4799   Thymidylate Synthase Activity  Catalysis of the Reaction: 5 10 Methylenetetrahydrofolate + Dump = 7 8 Dihydrofolate + Thymidylate. 
    5542   Folic Acid Binding  Interacting Selectively and Non Covalently with Folic Acid Pteroylglutamic Acid. Folic Acid Is Widely Distributed As a Member of the Vitamin B Complex and Is Essential For the Synthesis of Purine and Pyrimidines. 
    8144   Drug Binding  Interacting Selectively and Non Covalently with a Drug Any Naturally Occurring or Synthetic Substance Other Than a Nutrient That When Administered or Applied to an Organism Affects the Structure or Functioning of the Organism; in Particular Any Such Substance Used in the Diagnosis Prevention or Treatment of Disease. 
    8168   Methyltransferase Activity  Catalysis of the Transfer of a Methyl Group to an Acceptor Molecule. 
    16740   Transferase Activity  Catalysis of the Transfer of a Group E.g. a Methyl Group Glycosyl Group Acyl Group Phosphorus Containing or Other Groups From One Compound (generally Regarded As the Donor) to Another Compound (generally Regarded As the Acceptor). Transferase Is the Systematic Name For Any Enzyme of EC Class 2. 
    42803   Protein Homodimerization Activity  Interacting Selectively and Non Covalently with an Identical Protein to Form a Homodimer. 
    48037   Cofactor Binding  Interacting Selectively and Non Covalently with a Cofactor a Substance That Is Required For the Activity of an Enzyme or Other Protein. Cofactors May Be Inorganic Such As the Metal Atoms Zinc Iron and Copper in Certain Forms or Organic in Which Case They Are Referred to As Coenzymes. Cofactors May Either Be Bound Tightly to Active Sites or Bind Loosely with the Substrate. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene tyms, ts, ok/sw-cl.29
    Host Scientific Name Escherichia coli  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    18 18p11.32 7298     thymidylate synthetase TYMS    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs139713318 LS-SNP   dbSNP   A 78 R - > C Coil 50% (Exposed) 18 659667
    rs59755869 LS-SNP   dbSNP   A 100 E - > Q Helix 30% (Intermediate) 18 662164
    rs201415512 LS-SNP   dbSNP   A 134 V - > D Coil 16% (Intermediate) 18 662267
    rs200442141 LS-SNP   dbSNP   A 147 R - > K Coil 59% (Exposed) 18 662306
    rs141666868 LS-SNP   dbSNP   A 148 D - > E Coil 43% (Exposed) 18 662310
    rs596909 LS-SNP   dbSNP   A 157 G - > V Bend 50% (Exposed) 18 669087
    rs11540153 LS-SNP   dbSNP   A 167 T - > I Helix 20% (Intermediate) 18 669117
    rs147052596 LS-SNP   dbSNP   A 170 T - > S Helix 77% (Exposed) 18 669126
    rs201232749 LS-SNP   dbSNP   A 216 S - > L Beta Ladder 33% (Intermediate) 18 670782