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CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH 2(S)-AMINO-6-BORONOHEXANOIC ACID, AN L-ARGININE ANALOG
Biology and Chemistry Report
1D3V
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE
    Text BINUCLEAR MANGANESE CLUSTER, BORONIC ACID INHIBITOR, PERFECTLY TWINNED CRYSTAL, HYDROLASE

    Polymeric Molecules

    Chain A,B
    Description PROTEIN (ARGINASE) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 35019.4 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ABH  2(S)-AMINO-6-BORONOHEXANOIC ACID  C6 H15 B N O5   192.00  View 
    MN  MANGANESE (II) ION  Mn   54.94  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B ARGI1_RAT P07824     

    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. 
    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. 
    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). 
    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. 
    19547   Arginine Catabolic Process to Ornithine  The Chemical Reactions and Pathways Resulting in the Breakdown of Arginine Into Other Compounds Including Ornithine. 
    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. 
    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. 
    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. 
    5741   Mitochondrial Outer Membrane  The Outer I.e. Cytoplasm Facing Lipid Bilayer of the Mitochondrial Envelope. 
    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 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. Extracellular Exosomes Also Simply Called Exosomes Have a Diameter of About 40 100 Nm. 
    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 Norway Rat
    Scientific Name Rattus norvegicus  
    Genus Rattus
    Organ Liver
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Vector Rset C
    Host Vector Type Plasmid


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    1 1p12 29221     arginase 1 ARG1