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(-) Description

Title :  CRYSTAL STRUCTURE OF DIRAS2 IN COMPLEX WITH GDP AND INORGANIC PHOSPHATE
 
Authors :  E. Papagrigoriou, X. Yang, J. Elkins, F. E. Niesen, N. Burgess, E. Salah, O. Fedorov, L. J. Ball, F. Von Delft, M. Sundstrom, A. Edwards, C. Arrowsmith, J. Weigelt, D. Doyle
Date :  25 Oct 05  (Deposition) - 01 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Diras2, Gtp Hydrolysis, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Papagrigoriou, X. Yang, J. Elkins, F. E. Niesen, N. Burgess, E. Salah, O. Fedorov, L. J. Ball, F. Von Delft, M. Sundstrom, A. Edwards, C. Arrowsmith, J. Weigelt, D. Doyle
Crystal Structure Of Diras2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GTP-BINDING PROTEIN DI-RAS2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)R3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDIRAS2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDISTINCT SUBGROUP OF THE RAS FAMILY MEMBER 2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:16 , LYS B:20 , TYR B:36 , THR B:39 , THR B:63 , GLY B:64 , SER B:65 , GDP B:401 , MG B:403 , HOH B:477 , HOH B:483BINDING SITE FOR RESIDUE PO4 B 402
2AC2SOFTWARESER B:21 , THR B:39 , GDP B:401 , PO4 B:402 , HOH B:477 , HOH B:483BINDING SITE FOR RESIDUE MG B 403
3AC3SOFTWAREGLY A:16 , LYS A:20 , TYR A:36 , THR A:39 , THR A:63 , GLY A:64 , GDP A:401 , MG A:403 , HOH A:494 , HOH A:495BINDING SITE FOR RESIDUE PO4 A 402
4AC4SOFTWARESER A:21 , THR A:39 , GDP A:401 , PO4 A:402 , HOH A:494 , HOH A:495BINDING SITE FOR RESIDUE MG A 403
5AC5SOFTWAREGLY B:17 , VAL B:18 , GLY B:19 , LYS B:20 , SER B:21 , SER B:22 , PHE B:32 , ARG B:33 , GLU B:34 , TYR B:36 , ASN B:121 , LYS B:122 , ASP B:124 , GLU B:125 , SER B:151 , ALA B:152 , LYS B:153 , PO4 B:402 , MG B:403 , HOH B:407 , HOH B:414 , HOH B:440 , HOH B:477 , HOH B:483 , HOH B:492BINDING SITE FOR RESIDUE GDP B 401
6AC6SOFTWAREGLY A:17 , VAL A:18 , GLY A:19 , LYS A:20 , SER A:21 , SER A:22 , PHE A:32 , ARG A:33 , GLU A:34 , TYR A:36 , ASN A:121 , LYS A:122 , ASP A:124 , GLU A:125 , SER A:151 , ALA A:152 , LYS A:153 , PO4 A:402 , MG A:403 , HOH A:445 , HOH A:464 , HOH A:486 , HOH A:494 , HOH A:495BINDING SITE FOR RESIDUE GDP A 401

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:50 -B:55

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ERX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ERX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ERX)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003757651ENSE00001468331chr9:93405386-93405034353DIRA2_HUMAN-00--
1.2ENST000003757652ENSE00001468329chr9:93376145-933721144032DIRA2_HUMAN1-2112112A:6-176 (gaps)
B:5-176 (gaps)
171
172

(-) Sequences/Alignments

Asymmetric 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:168
 aligned with DIRA2_HUMAN | Q96HU8 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:171
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175 
          DIRA2_HUMAN     6 NDYRVAVFGAGGVGKSSLVLRFVKGTFRESYIPTVEDTYRQVISCDKSICTLQITDTTGSHQFPAMQRLSISKGHAFILVYSITSRQSLEELKPIYEQICEIKGDVESIPIMLVGNKCDESPSREVQSSEAEALARTWKCAFMETSAKLNHNVKELFQELLNLEKRRTVSL 176
               SCOP domains d2erxa1 A:6-176 di-Ras2                                                                                                                                                     SCOP domains
               CATH domains 2erxA00 A:6-176 P-loop containing nucleotide triphosphate hydrolases                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhh............eeeeeeeee..eeeeeeeee......hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh---...eeeeeehhhhhhhh..hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: A:6-176 (gaps) UniProt: 1-211 [INCOMPLETE]                                                                                                                   Transcript 1
                 2erx A   6 NDYRVAVFGAGGVGKSSLVLRFVKGTFRESYIPTVEDTYRQVISCDKSICTLQITDTTGSHQFPAMQRLSISKGHAFILVYSITSRQSLEELKPIYEQICEIKG---SIPIMLVGNKCDESPSREVQSSEAEALARTWKCAFMETSAKLNHNVKELFQELLNLEKRRTVSL 176
                                    15        25        35        45        55        65        75        85        95       105   |   115       125       135       145       155       165       175 
                                                                                                                                 109 113                                                               

Chain B from PDB  Type:PROTEIN  Length:166
 aligned with DIRA2_HUMAN | Q96HU8 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:172
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  
          DIRA2_HUMAN     5 SNDYRVAVFGAGGVGKSSLVLRFVKGTFRESYIPTVEDTYRQVISCDKSICTLQITDTTGSHQFPAMQRLSISKGHAFILVYSITSRQSLEELKPIYEQICEIKGDVESIPIMLVGNKCDESPSREVQSSEAEALARTWKCAFMETSAKLNHNVKELFQELLNLEKRRTVSL 176
               SCOP domains d2erxb_ B: automated matches                                                                                                                                                 SCOP domains
               CATH domains 2erxB00 B:5-176 P-loop containing nucleotide t  riphosphate hydrolases                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhh...........eeeeeee..--..eeeeeee......hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh----...eeeeee...hhhhh..hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: B:5-176 (gaps) UniProt: 1-211 [INCOMPLETE]                                                                                                                    Transcript 1
                 2erx B   5 SNDYRVAVFGAGGVGKSSLVLRFVKGTFRESYIPTVEDTYRQVISC--SICTLQITDTTGSHQFPAMQRLSISKGHAFILVYSITSRQSLEELKPIYEQICEIK----SIPIMLVGNKCDESPSREVQSSEAEALARTWKCAFMETSAKLNHNVKELFQELLNLEKRRTVSL 176
                                    14        24        34        44     |  54        64        74        84        94       104   |   114       124       134       144       154       164       174  
                                                                        50 53                                                    108  113                                                               

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ERX)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DIRA2_HUMAN | Q96HU8)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0000166    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.
biological process
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    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.
cellular component
    GO:0005622    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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