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Crystal structure of native, unliganded human arginase at 1.90 resolution
Biology and Chemistry Report
2PHA
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE
    Text PROTON WIRE, HYDROLASE

    Polymeric Molecules

    Chain A,B
    Description Arginase-1 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 34780.2 
    Source Method genetically manipulated  
    Entity Name Type I arginase, Liver-type arginase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    MN  MANGANESE (II) ION  Mn   54.94  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B ARGI1_HUMAN A6NEA0     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc Catalytic Site(s)
    A B  3.5.3.1        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    50   Urea Cycle  The Sequence of Reactions by Which Arginine Is Synthesized From Ornithine Then Cleaved to Yield Urea and Regenerate Ornithine. the Overall Reaction Equation Is Nh3 + Co2 + Aspartate + 3 ATP + 2 H2o = Urea + Fumarate + 2 Adp + 2 Phosphate + AMP + Diphosphate. 
    1889   Liver Development  The Process Whose Specific Outcome Is the Progression of the Liver Over Time From Its Formation to the Mature Structure. the Liver Is an Exocrine Gland Which Secretes Bile and Functions in Metabolism of Protein and Carbohydrate and Fat Synthesizes Substances Involved in the Clotting of the Blood Synthesizes Vitamin a Detoxifies Poisonous Substances Stores Glycogen and Breaks Down Worn Out Erythrocytes. 
    1938   Positive Regulation of Endothelial Cell Proliferation  Any Process That Activates or Increases the Rate or Extent of Endothelial Cell Proliferation. 
    6525   Arginine Metabolic Process  The Chemical Reactions and Pathways Involving Arginine 2 Amino 5 (carbamimidamido)pentanoic Acid. 
    6527   Arginine Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Arginine 2 Amino 5 (carbamimidamido)pentanoic Acid. 
    7565   Female Pregnancy  The Set of Physiological Processes That Allow an Embryo or Foetus to Develop Within the Body of a Female Animal. It Covers the Time From Fertilization of a Female Ovum by a Male Spermatozoon Until Birth. 
    9611   Response to Wounding  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 Indicating Damage to the Organism. 
    9635   Response to Herbicide  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 Herbicide Stimulus. Herbicides Are Chemicals Used to Kill or Control the Growth of Plants. 
    10042   Response to Manganese Ion  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 Manganese Ion Stimulus. 
    10043   Response to Zinc Ion  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 Zinc Ion Stimulus. 
    10269   Response to Selenium Ion  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 From Selenium Ion. 
    10963   Regulation of L Arginine Import  Any Process That Modulates the Frequency Rate or Extent of L Arginine Import. L Arginine Import Is the Directed Movement of L Arginine the L Enantiomer of 2 Amino 5 Guanidinopentanoic Acid Into a Cell or Organelle. 
    14075   Response to Amine  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 Amine Stimulus. an Amine Is a Compound Formally Derived From Ammonia by Replacing One Two or Three Hydrogen Atoms by Hydrocarbyl Groups. 
    30324   Lung Development  The Process Whose Specific Outcome Is the Progression of the Lung Over Time From Its Formation to the Mature Structure. in All Air Breathing Vertebrates the Lungs Are Developed From the Ventral Wall of the Oesophagus As a Pouch Which Divides Into Two Sacs. in Amphibians and Many Reptiles the Lungs Retain Very Nearly This Primitive Sac Like Character But in the Higher Forms the Connection with the Esophagus Becomes Elongated Into the Windpipe and the Inner Walls of the Sacs Become More and More Divided Until in the Mammals the Air Spaces Become Minutely Divided Into Tubes Ending in Small Air Cells in the Walls of Which the Blood Circulates in a Fine Network of Capillaries. in Mammals the Lungs Are More or Less Divided Into Lobes and Each Lung Occupies a Separate Cavity in the Thorax. 
    32496   Response to Lipopolysaccharide  Any Process That Results in a Change in State or Activity of an Organism (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Lipopolysaccharide Stimulus; Lipopolysaccharide Is a Major Component of the Cell Wall of Gram Negative Bacteria. 
    32964   Collagen Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Collagen Any of a Group of Fibrous Proteins of Very High Tensile Strength That Form the Main Component of Connective Tissue in Animals. Collagen Is Highly Enriched in Glycine (some Regions Are 33% Glycine) and Proline Occurring Predominantly As 3 Hydroxyproline (about 20%). 
    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. 
    33197   Response to Vitamin E  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 E Stimulus. 
    34641   Cellular Nitrogen Compound Metabolic Process  The Chemical Reactions and Pathways Involving Various Organic and Inorganic Nitrogenous Compounds As Carried Out by Individual Cells. 
    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. 
    43200   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. 
    43434   Response to Peptide Hormone  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 Peptide Hormone Stimulus. a Peptide Hormone Is Any of a Class of Peptides That Are Secreted Into the Blood Stream and Have Endocrine Functions in Living Animals. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    46686   Response to Cadmium Ion  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 Cadmium (cd) Ion Stimulus. 
    48545   Response to Steroid Hormone  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 Steroid Hormone Stimulus. 
    48678   Response to Axon Injury  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 Axon Injury Stimulus. 
    51597   Response to Methylmercury  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 Methylmercury Stimulus. 
    60056   Mammary Gland Involution  The Tissue Remodeling That Removes Differentiated Mammary Epithelia During Weaning. 
    60135   Maternal Process Involved in Female Pregnancy  A Reproductive Process Occurring in the Mother That Allows an Embryo or Fetus to Develop Within It. 
    70207   Protein Homotrimerization  The Formation of a Protein Homotrimer a Macromolecular Structure Consisting of Three Noncovalently Associated Identical Subunits. 
    70301   Cellular Response to Hydrogen Peroxide  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Hydrogen Peroxide (h2o2) Stimulus. 
    71222   Cellular Response to Lipopolysaccharide  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Lipopolysaccharide Stimulus; Lipopolysaccharide Is a Major Component of the Cell Wall of Gram Negative Bacteria. 
    71353   Cellular Response to Interleukin 4  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of an Interleukin 4 Stimulus. 
    71377   Cellular Response to Glucagon Stimulus  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Glucagon Stimulus. 
    71549   Cellular Response to Dexamethasone Stimulus  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Dexamethasone Stimulus. 
    71560   Cellular Response to Transforming Growth Factor Beta Stimulus  Any Process That Results in a Change in State or Activity of a Cell (in Terms of Movement Secretion Enzyme Production Gene Expression Etc.) As a Result of a Transforming Growth Factor Beta Stimulus. 
    5615   Extracellular Space  That Part of a Multicellular Organism Outside the Cells Proper Usually Taken to Be Outside the Plasma Membranes and Occupied by Fluid. 
    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. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    43005   Neuron Projection  A Prolongation or Process Extending From a Nerve Cell E.g. an Axon or Dendrite. 
    43025   Neuronal Cell Body  The Portion of a Neuron That Includes the Nucleus But Excludes Cell Projections Such As Axons and Dendrites. 
    70062   Extracellular Vesicular Exosome  A Membrane Bounded Vesicle That Is Released Into the Extracellular Region by Fusion of the Limiting Endosomal Membrane of a Multivesicular Body with the Plasma Membrane. 
    4053   Arginase Activity  Catalysis of the Reaction: L Arginine + H2o = L Ornithine + Urea. 
    16787   Hydrolase Activity  Catalysis of the Hydrolysis of Various Bonds E.g. C O C N C C Phosphoric Anhydride Bonds Etc. Hydrolase Is the Systematic Name For Any Enzyme of EC Class 3. 
    16813   Hydrolase Activity Acting On Carbon Nitrogen (but Not Peptide) Bonds in Linear Amidines  Catalysis of the Hydrolysis of Any Non Peptide Carbon Nitrogen Bond in a Linear Amidine a Compound of the Form R C(=nh) Nh2. 
    30145   Manganese Ion Binding  Interacting Selectively and Non Covalently with Manganese (mn) Ions. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene arg1
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Vector Type Plasmid
    Host Plasmid Name pBS(KS)


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    6 6q23 383     arginase 1 ARG1    

    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
    rs149310631 LS-SNP   dbSNP   A 8 I - > K Beta Ladder 0% (Buried) 6 131894445
    rs28941474 LS-SNP   dbSNP   A 11 I - > T Beta Ladder 0% (Buried) 6 131894454
    rs147419581 LS-SNP   dbSNP   A 12 G - > A Beta Ladder 0% (Buried) 6 131894457
    rs144994895 LS-SNP   dbSNP   A 21 R - > Q Coil 14% (Intermediate) 6 131897807
    rs11544411 LS-SNP   dbSNP   A 26 E - > G Turn 39% (Exposed) 6 131897822
    rs147146526 LS-SNP   dbSNP   A 57 D - > G Coil 77% (Exposed) 6 131900290
    rs111640755 LS-SNP   dbSNP   A 62 S - > N Coil 20% (Intermediate) 6 131900305
    rs148619575 LS-SNP   dbSNP   A 79 Q - > H Helix 15% (Intermediate) 6 131900357
    rs142107090 LS-SNP   dbSNP   A 81 A - > S Helix 0% (Buried) 6 131900361
    rs1063493 LS-SNP   dbSNP   A 86 E - > Q Helix 46% (Exposed) 6 131900376
    rs34724840 LS-SNP   dbSNP   A 94 S - > T Beta Ladder 0% (Buried) 6 131900401
    rs140549609 LS-SNP   dbSNP   A 128 D - > G Coil 6% (Buried) 6 131902436 MN
    rs104893943 LS-SNP   dbSNP   A 138 G - > V Coil 0% (Buried) 6 131902466
    rs200319835 LS-SNP   dbSNP   A 156 I - > T Bend 21% (Intermediate) 6 131903762
    rs201484132 LS-SNP   dbSNP   A 161 G - > A Turn 33% (Intermediate) 6 131903777
    rs201926198 LS-SNP   dbSNP   A 179 L - > F Coil 2% (Buried) 6 131903832
    rs141449121 LS-SNP   dbSNP   A 185 G - > R Helix 32% (Intermediate) 6 131903848
    rs200496725 LS-SNP   dbSNP   A 214 E - > K Helix 25% (Intermediate) 6 131904279
    rs145177175 LS-SNP   dbSNP   A 222 R - > K Bend 92% (Exposed) 6 131904304
    rs104893948 LS-SNP   dbSNP   A 235 G - > R 3/10 Helix 0% (Buried) 6 131904532
    rs182650447 LS-SNP   dbSNP   A 249 V - > L Bend 86% (Exposed) 6 131904574
    rs111253965 LS-SNP   dbSNP   A 266 K - > N Helix 68% (Exposed) 6 131904627
    rs104893942 LS-SNP   dbSNP   A 290 T - > S Helix 53% (Exposed) 6 131904948
    rs148113697 LS-SNP   dbSNP   A 303 C - > G Helix 1% (Buried) 6 131904986
    rs202219126 LS-SNP   dbSNP   A 315 I - > T Bend 72% (Exposed) 6 131905023
    rs73544627 LS-SNP   dbSNP   A 318 L - > P Coil 118% (Exposed) 6 131905032