POP-OUT | CLOSE
 
Crystal structure of RAC1 Q61L mutant
Biology and Chemistry Report
4GZL
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE
    Text Rossmann fold, GTP binding, membrane, HYDROLASE

    Polymeric Molecules

    Chain A,B
    Description Ras-related C3 botulinum toxin substrate 1 
    Fragment UNP residues 2-177 
    Mutation Q61L 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 22719.2 
    Source Method genetically manipulated  
    Entity Name RAC1, Cell migration-inducing gene 5 protein, Ras-like protein TC25, p21-Rac1 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    GNP  PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER  C10 H17 N6 O13 P3   522.20  View 
    IPA  ISOPROPYL ALCOHOL  C3 H8 O   60.10  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B RAC1_HUMAN O95501     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  3.6.5.2      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    1934   Positive Regulation of Protein Phosphorylation  Any Process That Activates or Increases the Frequency Rate or Extent of Addition of Phosphate Groups to Amino Acids Within a Protein. 
    2093   Auditory Receptor Cell Morphogenesis  Any Process That Alters the Size or Shape of an Auditory Receptor Cell. 
    2551   Mast Cell Chemotaxis  The Movement of a Mast Cell in Response to an External Stimulus. 
    3382   Epithelial Cell Morphogenesis  The Change in Form That Occurs When an Epithelial Cell Progresses From Its Initial Formation to Its Mature State. 
    6184   GTP Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of GTP Guanosine Triphosphate. 
    6897   Endocytosis  A Vesicle Mediated Transport Process in Which Cells Take Up External Materials or Membrane Constituents by the Invagination of a Small Region of the Plasma Membrane to Form a New Membrane Bounded Vesicle. 
    6911   Phagocytosis Engulfment  The Internalization of Bacteria Immune Complexes and Other Particulate Matter or of an Apoptotic Cell by Phagocytosis Including the Membrane and Cytoskeletal Processes Required Which Involves One of Three Mechanisms: Zippering of Pseudopods Around a Target Via Repeated Receptor Ligand Interactions Sinking of the Target Directly Into Plasma Membrane of the Phagocytosing Cell or Induced Uptake Via an Enhanced Membrane Ruffling of the Phagocytosing Cell Similar to Macropinocytosis. 
    6928   Cellular Component Movement  The Directed Self Propelled Movement of a Cellular Component Without the Involvement of an External Agent Such As a Transporter or a Pore. 
    6935   Chemotaxis  The Directed Movement of a Motile Cell or Organism or the Directed Growth of a Cell Guided by a Specific Chemical Concentration Gradient. Movement May Be Towards a Higher Concentration (positive Chemotaxis) or Towards a Lower Concentration (negative Chemotaxis). 
    6954   Inflammatory Response  The Immediate Defensive Reaction (by Vertebrate Tissue) to Infection or Injury Caused by Chemical or Physical Agents. the Process Is Characterized by Local Vasodilation Extravasation of Plasma Into Intercellular Spaces and Accumulation of White Blood Cells and Macrophages. 
    6972   Hyperosmotic Response  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 Detection of or Exposure to a Hyperosmotic Environment I.e. an Environment with a Higher Concentration of Solutes Than the Organism or Cell. 
    7010   Cytoskeleton Organization  A Process That Is Carried Out At the Cellular Level Which Results in the Assembly Arrangement of Constituent Parts or Disassembly of Cytoskeletal Structures. 
    7015   Actin Filament Organization  A Process That Is Carried Out At the Cellular Level Which Results in the Assembly Arrangement of Constituent Parts or Disassembly of Cytoskeletal Structures Comprising Actin Filaments. Includes Processes That Control the Spatial Distribution of Actin Filaments Such As Organizing Filaments Into Meshworks Bundles or Other Structures As by Cross Linking. 
    7155   Cell Adhesion  The Attachment of a Cell Either to Another Cell or to an Underlying Substrate Such As the Extracellular Matrix Via Cell Adhesion Molecules. 
    7160   Cell Matrix Adhesion  The Binding of a Cell to the Extracellular Matrix Via Adhesion Molecules. 
    7186   G Protein Coupled Receptor Signaling Pathway  A Series of Molecular Signals That Proceeds with an Activated Receptor Promoting the Exchange of GDP For GTP On the Alpha Subunit of an Associated Heterotrimeric G Protein Complex. the GTP Bound Activated Alpha G Protein Then Dissociates From the Beta and Gamma Subunits to Further Transmit the Signal Within the Cell. the Pathway Begins with Receptor Ligand Interaction or For Basal Gpcr Signaling the Pathway Begins with the Receptor Activating Its G Protein in the Absence of an Agonist and Ends with Regulation of a Downstream Cellular Process E.g. Transcription. 
    7264   Small Gtpase Mediated Signal Transduction  Any Series of Molecular Signals in Which a Small Monomeric Gtpase Relays One or More of the Signals. 
    7411   Axon Guidance  The Chemotaxis Process That Directs the Migration of an Axon Growth Cone to a Specific Target Site in Response to a Combination of Attractive and Repulsive Cues. 
    7596   Blood Coagulation  The Sequential Process in Which the Multiple Coagulation Factors of the Blood Interact Ultimately Resulting in the Formation of an Insoluble Fibrin Clot; It May Be Divided Into Three Stages: Stage 1 the Formation of Intrinsic and Extrinsic Prothrombin Converting Principle; Stage 2 the Formation of Thrombin; Stage 3 the Formation of Stable Fibrin Polymers. 
    8283   Cell Proliferation  The Multiplication or Reproduction of Cells Resulting in the Expansion of a Cell Population. 
    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. 
    9653   Anatomical Structure Morphogenesis  The Process in Which Anatomical Structures Are Generated and Organized. Morphogenesis Pertains to the Creation of Form. 
    10310   Regulation of Hydrogen Peroxide Metabolic Process  Any Process That Modulates the Frequency Rate or Extent of the Chemical Reactions and Pathways Involving Hydrogen Peroxide. 
    10592   Positive Regulation of Lamellipodium Assembly  Any Process That Increases the Rate Frequency or Extent of the Formation of a Lamellipodium a Thin Sheetlike Extension of the Surface of a Migrating Cell. 
    16032   Viral Process  A Multi Organism Process in Which a Virus Is a Participant. the Other Participant Is the Host. Includes Infection of a Host Cell Replication of the Viral Genome and Assembly of Progeny Virus Particles. in Some Cases the Viral Genetic Material May Integrate Into the Host Genome and Only Subsequently Under Particular Circumstances 'complete' Its Life Cycle. 
    16358   Dendrite Development  The Process Whose Specific Outcome Is the Progression of the Dendrite Over Time From Its Formation to the Mature Structure. a Dendrite Is a Freely Branching Protoplasmic Process of a Nerve Cell. 
    16477   Cell Migration  The Controlled Self Propelled Movement of a Cell From One Site to a Destination Guided by Molecular Cues. Cell Migration Is a Central Process in the Development and Maintenance of Multicellular Organisms. 
    21799   Cerebral Cortex Radially Oriented Cell Migration  The Migration of Cells in the Developing Cerebral Cortex in Which Cells Move From the Ventricular And/or Subventricular Zone Toward the Surface of the Brain. 
    21831   Embryonic Olfactory Bulb Interneuron Precursor Migration  The Directed Movement of Individual Interneuron Precursors During the Embryonic Development of the Olfactory Bulb. 
    30032   Lamellipodium Assembly  Formation of a Lamellipodium a Thin Sheetlike Extension of the Surface of a Migrating Cell. 
    30036   Actin Cytoskeleton Organization  A Process That Is Carried Out At the Cellular Level Which Results in the Assembly Arrangement of Constituent Parts or Disassembly of Cytoskeletal Structures Comprising Actin Filaments and Their Associated Proteins. 
    30041   Actin Filament Polymerization  Assembly of Actin Filaments by the Addition of Actin Monomers to a Filament. 
    30168   Platelet Activation  A Series of Progressive Overlapping Events Triggered by Exposure of the Platelets to Subendothelial Tissue. These Events Include Shape Change Adhesiveness Aggregation and Release Reactions. When Carried Through to Completion These Events Lead to the Formation of a Stable Hemostatic Plug. 
    30334   Regulation of Cell Migration  Any Process That Modulates the Frequency Rate or Extent of Cell Migration. 
    30838   Positive Regulation of Actin Filament Polymerization  Any Process That Activates or Increases the Frequency Rate or Extent of Actin Polymerization. 
    31295   T Cell Costimulation  The Process of Providing Via Surface Bound Receptor Ligand Pairs a Second Antigen Independent Signal in Addition to That Provided by the T Cell Receptor to Augment T Cell Activation. 
    31529   Ruffle Organization  A Process That Is Carried Out At the Cellular Level Which Results in the Assembly Arrangement of Constituent Parts or Disassembly of a Ruffle a Projection At the Leading Edge of a Crawling Cell. 
    32707   Negative Regulation of Interleukin 23 Production  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Interleukin 23 Production. 
    34446   Substrate Adhesion Dependent Cell Spreading  The Morphogenetic Process That Results in Flattening of a Cell As a Consequence of Its Adhesion to a Substrate. 
    35025   Positive Regulation of Rho Protein Signal Transduction  Any Process That Activates or Increases the Frequency Rate or Extent of Rho Protein Signal Transduction. 
    35556   Intracellular Signal Transduction  The Process in Which a Signal Is Passed On to Downstream Components Within the Cell Which Become Activated Themselves to Further Propagate the Signal and Finally Trigger a Change in the Function or State of the Cell. 
    38095   Fc Epsilon Receptor Signaling Pathway  A Series of Molecular Signals Initiated by the Binding of the Fc Portion of Immunoglobulin E (ige) to an Fc Epsilon Receptor On the Surface of a Signal Receiving Cell and Ending with Regulation of a Downstream Cellular Process E.g. Transcription. the Fc Portion of an Immunoglobulin Is Its C Terminal Constant Region. 
    38096   Fc Gamma Receptor Signaling Pathway Involved in Phagocytosis  An Fc Gamma Receptor Signaling Pathway That Contributes to the Endocytic Engulfment of External Particulate Material by Phagocytes. 
    43065   Positive Regulation of Apoptotic Process  Any Process That Activates or Increases the Frequency Rate or Extent of Cell Death by Apoptotic Process. 
    43552   Positive Regulation of Phosphatidylinositol 3 Kinase Activity  Any Process That Activates or Increases the Frequency Rate or Extent of Phosphatidylinositol 3 Kinase Activity. 
    43652   Engulfment of Apoptotic Cell  The Removal of the Apoptotic Cell by Phagocytosis by a Neighboring Cell or by a Phagocyte. 
    45087   Innate Immune Response  Innate Immune Responses Are Defense Responses Mediated by Germline Encoded Components That Directly Recognize Components of Potential Pathogens. 
    45216   Cell Cell Junction Organization  A Process That Is Carried Out At the Cellular Level Which Results in the Assembly Arrangement of Constituent Parts or Disassembly of a Cell Cell Junction. a Cell Cell Junction Is a Specialized Region of Connection Between Two Cells. 
    45453   Bone Resorption  The Process in Which Specialized Cells Known As Osteoclasts Degrade the Organic and Inorganic Portions of Bone and Endocytose and Transport the Degradation Products. 
    45740   Positive Regulation of DNA Replication  Any Process That Activates or Increases the Frequency Rate or Extent of DNA Replication. 
    48011   Neurotrophin Trk Receptor Signaling Pathway  A Series of Molecular Signals Initiated by the Binding of a Neurotrophin to a Receptor On the Surface of the Target Cell Where the Receptor Possesses Tyrosine Kinase Activity and Ending with Regulation of a Downstream Cellular Process E.g. Transcription. 
    48261   Negative Regulation of Receptor Mediated Endocytosis  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Receptor Mediated Endocytosis the Uptake of External Materials by Cells Utilizing Receptors to Ensure Specificity of Transport. 
    48532   Anatomical Structure Arrangement  The Process That Gives Rise to the Configuration of the Constituent Parts of an Anatomical Structure. This Process Pertains to the Physical Shaping of a Rudimentary Structure. Anatomical Structures Can Be Macroscopic Such As a Carpel or Microscopic Such As an Acrosome. 
    48813   Dendrite Morphogenesis  The Process in Which the Anatomical Structures of a Dendrite Are Generated and Organized. a Dendrite Is a Freely Branching Protoplasmic Process of a Nerve Cell. 
    48870   Cell Motility  Any Process Involved in the Controlled Self Propelled Movement of a Cell That Results in Translocation of the Cell From One Place to Another. 
    50690   Regulation of Defense Response to Virus by Virus  Any Viral Process That Modulates the Frequency Rate or Extent of the Antiviral Response of the Host Cell or Organism. 
    51496   Positive Regulation of Stress Fiber Assembly  Any Process That Activates or Increases the Frequency Rate or Extent of the Assembly of a Stress Fiber a Bundle of Microfilaments and Other Proteins Found in Fibroblasts. 
    51668   Localization Within Membrane  Any Process in Which a Substance or Cellular Entity Such As a Protein Complex or Organelle Is Transported to And/or Maintained in a Specific Location Within a Membrane. 
    51894   Positive Regulation of Focal Adhesion Assembly  Any Process That Activates or Increases the Frequency Rate or Extent of Focal Adhesion Assembly the Establishment and Maturation of Focal Adhesions. 
    60071   Wnt Signaling Pathway Planar Cell Polarity Pathway  The Series of Molecular Signals Initiated by Binding of a Wnt Protein to a Receptor On the Surface of the Target Cell Where Activated Receptors Signal Via Downstream Effectors Including C Jun N Terminal Kinase (jnk) to Modulate Cytoskeletal Elements and Control Cell Polarity. 
    60263   Regulation of Respiratory Burst  Any Process That Modulates the Rate Frequency or Extent of a Phase of Elevated Metabolic Activity During Which Oxygen Consumption Increases; This Leads to the Production by an Nadh Dependent System of Hydrogen Peroxide (h2o2) Superoxide Anions and Hydroxyl Radicals. 
    71526   Semaphorin Plexin Signaling Pathway  A Series of Molecular Signals Generated As a Consequence of a Semaphorin Receptor (composed of a Plexin and a Neurophilin) Binding to a Semaphorin Ligand. 
    71542   Dopaminergic Neuron Differentiation  The Process in Which a Neuroblast Acquires the Specialized Structural and Functional Features of a Dopaminergic Neuron a Neuron That Secretes Dopamine. 
    72659   Protein Localization to Plasma Membrane  A Process in Which a Protein Is Transported to or Maintained in a Specific Location in the Plasma Membrane. 
    90103   Cochlea Morphogenesis  The Process in Which the Cochlea Is Generated and Organized. 
    97178   Ruffle Assembly  The Aggregation Arrangement and Bonding Together of a Set of Components to Form a Ruffle a Projection At the Leading Edge of a Crawling Cell; the Protrusions Are Supported by a Microfilament Meshwork. the Formation of Ruffles (also Called Membrane Ruffling) Is Thought to Be Controlled by a Group of Enzymes Known As Rho Gtpases Specifically Rhoa Rac1 and Cdc42. 
    97190   Apoptotic Signaling Pathway  A Series of Molecular Signals Which Triggers the Apoptotic Death of a Cell. the Pathway Starts with Reception of a Signal and Ends When the Execution Phase of Apoptosis Is Triggered. 
    1900026   Positive Regulation of Substrate Adhesion Dependent Cell Spreading  Any Process That Activates or Increases the Frequency Rate or Extent of Substrate Adhesion Dependent Cell Spreading. 
    139   Golgi Membrane  The Lipid Bilayer Surrounding Any of the Compartments of the Golgi Apparatus. 
    1891   Phagocytic Cup  An Invagination of the Cell Membrane Formed by an Actin Dependent Process During Phagocytosis. Following Internalization It Is Converted Into a Phagosome. 
    5622   Intracellular  The Living Contents of a Cell; the Matter Contained Within (but Not Including) the Plasma Membrane Usually Taken to Exclude Large Vacuoles and Masses of Secretory or Ingested Material. in Eukaryotes It Includes the Nucleus and Cytoplasm. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5802   Trans Golgi Network  The Network of Interconnected Tubular and Cisternal Structures Located Within the Golgi Apparatus On the Side Distal to the Endoplasmic Reticulum From Which Secretory Vesicles Emerge. the Trans Golgi Network Is Important in the Later Stages of Protein Secretion Where It Is Thought to Play a Key Role in the Sorting and Targeting of Secreted Proteins to the Correct Destination. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    5886   Plasma Membrane  The Membrane Surrounding a Cell That Separates the Cell From Its External Environment. It Consists of a Phospholipid Bilayer and Associated Proteins. 
    5925   Focal Adhesion  Small Region On the Surface of a Cell That Anchors the Cell to the Extracellular Matrix and That Forms a Point of Termination of Actin Filaments. 
    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. 
    16023   Cytoplasmic Membrane Bounded Vesicle  A Membrane Bounded Vesicle Found in the Cytoplasm of the Cell. 
    19897   Extrinsic Component of Plasma Membrane  The Component of a Plasma Membrane Consisting of Gene Products and Protein Complexes That Are Loosely Bound to One of Its Surfaces But Not Integrated Into the Hydrophobic Region. 
    30027   Lamellipodium  A Thin Sheetlike Process Extended by the Leading Edge of a Crawling Fibroblast; Contains a Dense Meshwork of Actin Filaments. 
    31410   Cytoplasmic Vesicle  A Vesicle Formed of Membrane or Protein Found in the Cytoplasm of a Cell. 
    32587   Ruffle Membrane  The Portion of the Plasma Membrane Surrounding a Ruffle. 
    36464   Cytoplasmic Ribonucleoprotein Granule  A Ribonucleoprotein Granule Located in the Cytoplasm. 
    42470   Melanosome  A Tissue Specific Membrane Bounded Cytoplasmic Organelle Within Which Melanin Pigments Are Synthesized and Stored. Melanosomes Are Synthesized in Melanocyte Cells. 
    42995   Cell Projection  A Prolongation or Process Extending From a Cell E.g. a Flagellum or Axon. 
    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. 
    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. 
    3924   Gtpase Activity  Catalysis of the Reaction: GTP + H2o = GDP + Phosphate. 
    5515   Protein Binding  Interacting Selectively and Non Covalently with Any Protein or Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 
    5525   GTP Binding  Interacting Selectively and Non Covalently with GTP Guanosine Triphosphate. 
    17137   Rab Gtpase Binding  Interacting Selectively and Non Covalently with Rab Protein Any Member of the Rab Subfamily of the Ras Superfamily of Monomeric Gtpases. 
    19899   Enzyme Binding  Interacting Selectively and Non Covalently with Any Enzyme. 
    19901   Protein Kinase Binding  Interacting Selectively and Non Covalently with a Protein Kinase Any Enzyme That Catalyzes the Transfer of a Phosphate Group Usually From ATP to a Protein Substrate. 
    30742   GTP Dependent Protein Binding  Interacting Selectively and Non Covalently with Any Protein or Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules) Using Energy From the Hydrolysis of Gtp. 
    31996   Thioesterase Binding  Interacting Selectively and Non Covalently with Any Thioesterase Enzyme. 
    51022   Rho GDP Dissociation Inhibitor Binding  Interacting Selectively and Non Covalently with a Rho GDP Dissociation Inhibitor Protein. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene rac1, tc25, mig5
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)rilp
    Host Vector Type Plasmid
    Host Plasmid Name modified pET28


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    7 7p22 5879     ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) RAC1    

    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
    rs4521 LS-SNP   dbSNP   A 125 T - > AS Helix 17% (Intermediate) 7 6441583
    rs5828 LS-SNP   dbSNP   A 130 K - > R Helix 71% (Exposed) 7 6441599
    rs1804267 LS-SNP   dbSNP   A 132 K - > R Turn 79% (Exposed) 7 6441605
    rs5835 LS-SNP   dbSNP   A 133 K - > E Turn 89% (Exposed) 7 6441607
    rs11540455 LS-SNP   dbSNP   A 135 T - > I Coil 61% (Exposed) 7 6441614
    rs7657345 LS-SNP   dbSNP   A 165 L - > I Helix 1% (Buried) 7 6441991