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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RAS HOMOLOG DOMAIN OF HUMAN GRLF1 (P190RHOGAP)
 
Authors :  L. Shen, Y. Tong, W. Tempel, F. Mackenzie, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  31 Jan 08  (Deposition) - 12 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Ras, Gtpase, Glucorticoid Receptor, Structural Genomics Consortium, Sgc, Alternative Splicing, Anti-Oncogene, Cell Cycle, Cytoplasm, Dna-Binding, Gtpase Activation, Nucleus, Phosphoprotein, Repressor, Transcription, Transcription Regulation, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Shen, Y. Tong, W. Tempel, F. Mackenzie, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of The Ras Homolog Domain Of Human Grlf1 (P190Rhogap).
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCOCORTICOID RECEPTOR DNA-BINDING FACTOR 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21-CODONPLUS(DE3)-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRAS HOMOLOG DOMAIN: RESIDUES 13-249
    GeneGRLF1, GRF1, KIAA1722
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGLUCOCORTICOID RECEPTOR REPRESSION FACTOR 1, GRF- 1, RHO GAP P190A, P190-A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
3UNX5Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:36 , GLU A:95 , GNP A:301 , HOH A:389 , HOH A:390BINDING SITE FOR RESIDUE MG A 302
2AC2SOFTWAREHOH A:312 , HOH A:314 , HOH A:318 , HOH A:323 , HOH A:328 , HOH A:337BINDING SITE FOR RESIDUE MG A 303
3AC3SOFTWARELYS A:28 , GLY A:32 , ILE A:33 , GLY A:34 , LYS A:35 , SER A:36 , CYS A:37 , LEU A:52 , ASP A:53 , SER A:56 , GLU A:95 , THR A:97 , LYS A:201 , ASP A:203 , SER A:229 , ALA A:230 , ARG A:231 , MG A:302 , HOH A:311 , HOH A:316 , HOH A:319 , HOH A:389 , HOH A:390 , HOH A:394 , HOH A:395 , HOH A:396BINDING SITE FOR RESIDUE GNP A 301
4AC4SOFTWARETYR A:116 , ILE A:117BINDING SITE FOR RESIDUE UNX A 304
5AC5SOFTWAREVAL A:43 , ARG A:44 , MET A:132BINDING SITE FOR RESIDUE UNX A 305
6AC6SOFTWAREASN A:235 , ASP A:237 , LEU A:238BINDING SITE FOR RESIDUE UNX A 307
7AC7SOFTWAREPHE A:42 , ASP A:237BINDING SITE FOR RESIDUE UNX A 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C5H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C5H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C5H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C5H)

(-) Exons   (0, 0)

(no "Exon" information available for 3C5H)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:232
 aligned with RHG35_HUMAN | Q9NRY4 from UniProtKB/Swiss-Prot  Length:1499

    Alignment length:245
                                   13                                                                                                                                                                                                                                            
                                 12 |                                                                                                                                                                                                                                            
                                  | 14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244     
          RHG35_HUMAN     6 KQDVRIP-TYNISVVGLSGTEKEKGQCGIGKSCLCNRFVRPSADEFHLDHTSVLSTSDFGGRVVNNDHFLYWGEVSRSLEDCVECKMHIVEQTEFIDDQTFQPHRSTALQPYIKRAAATKLASAEKLMYFCTDQLGLEQDFEQKQMPDGKLLVDGFLLGIDVSRGMNRNFDDQLKFVSNLYNQLAKTKKPIVVVLTKCDEGVERYIRDAHTFALSKKNLQVVETSARSNVNVDLAFSTLVQLIDK 249
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee.............hhhhhhhhhhh............eehhhhhh........eeeeeee.---------.eeeeee...ee.......hhhhh.hhhhhhh..eee........hhhhh.hhhhh....hhh.eee..eeeeeee...----hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c5h A   5 RENLYFQGTYNISVVGLSGTEKEKGQCGIGKSCLCNRFVRPSADEFHLDHTSVLSTSDFGGRVVNNDHFLYWGEVS---------KMHIVEQTEFIDDQTFQPHRSTALQPYIKRAAATKLASAEKLMYFCTDQLGLEQDFEQKQMPDGKLLVDGFLLGIDVSR----NFDDQLKFVSNLYNQLAKTKKPIVVVLTKCDEGVERYIRDAHTFALSKKNLQVVETSARSNVNVDLAFSTLVQLIDK 249
                                    14        24        34        44        54        64        74     |   -     |  94       104       114       124       134       144       154       164   |   174       184       194       204       214       224       234       244     
                                                                                                      80        90                                                                           168  173                                                                            

   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 3C5H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3C5H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C5H)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RHG35_HUMAN | Q9NRY4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0001227    transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in the regulatory region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
    GO:0043010    camera-type eye development    The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
    GO:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0035024    negative regulation of Rho protein signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of Rho protein signal transduction.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0043116    negative regulation of vascular permeability    Any process that reduces the extent to which blood vessels can be pervaded by fluid.
    GO:0001843    neural tube closure    The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0051056    regulation of small GTPase mediated signal transduction    Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    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.

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 Related Entries

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        RHG35_HUMAN | Q9NRY42k85 3fk2

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