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(-) Description

Title :  X-RAY STRUCTURE OF NYSGRC TARGET T-45
 
Authors :  R. C. Deo, E. F. Schmidt, S. M. Strittmatter, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  11 Nov 01  (Deposition) - 05 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha/Beta Barrel, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. C. Deo, E. F. Schmidt, A. Elhabazi, H. Togashi, S. K. Burley, S. M. Strittmatter
Structural Bases For Crmp Function In Plexin-Dependent Semaphorin3A Signaling
Embo J. V. 23 9 2004
PubMed-ID: 14685275  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600021
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDROPYRIMIDINASE RELATED PROTEIN-1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6P1
    Expression System StrainUT5600
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 8-525
    GeneCRMP1 (8-525)
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymDRP-1, CRMP-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1KCX)

(-) Sites  (0, 0)

(no "Site" information available for 1KCX)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KCX)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:304 -Pro A:305
2Ser B:304 -Pro B:305

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KCX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KCX)

(-) Exons   (0, 0)

(no "Exon" information available for 1KCX)

(-) 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:476
 aligned with DPYL1_MOUSE | P97427 from UniProtKB/Swiss-Prot  Length:572

    Alignment length:476
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484      
          DPYL1_MOUSE    15 DRLLIRGGRIINDDQSFYADVYLEDGLIKQIGENLIVPGGVKTIEANGRMVIPGGIDVNTYLQKPSQGMTSADDFFQGTKAALAGGTTMIIDHVVPEPGSSLLTSFEKWHEAADTKSCCDYSLHVDITSWYDGVREELEVLVQDKGVNSFQVYMAYKDLYQMSDSQLYEAFTFLKGLGAVILVHAENGDLIAQEQKRILEMGITGPEGHALSRPEELEAEAVFRAIAIAGRINCPVYITKVMSKSAADIIALARKKGPLVFGEPIAASLGTDGTHYWSKNWAKAAAFVTSPPLSPDPTTPDYLTSLLACGDLQVTGSGHCPYSTAQKAVGKDNFTLIPEGVNGIEERMTVVWDKAVATGKMDENQFVAVTSTNAAKIFNLYPRKGRIAVGSDADVVIWDPDKMKTITAKSHKSTVEYNIFEGMECHGSPLVVISQGKIVFEDGNISVSKGMGRFIPRKPFPEHLYQRVRIRSKVFG 490
               SCOP domains d1kcxa1 A:15-66,A:401-490                           d1kcxa2 A:67-400 Dihydropyrimidinase related protein-1                                                                                                                                                                                                                                                                                        d1kcxa1 A:15-66,A:401-490 Dihydropyrimidinase related protein-1                            SCOP domains
               CATH domains 1kcxA01 A:15-67,A:441-490 Urease, subunit C, domain 11kcxA02 A:68-440 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                                                          1kcxA01 A:15-67,A:441-490                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eee....eee.eeeee..eeeeee.........eeee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee......hhhhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.hhhhhhhh..........hhhhhhhhhhhh.............hhhhhh....hhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh................eeeeeeeeeee..................eeeeeeeeeee..eeeee..ee...............hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kcx A  15 DRLLIRGGRIINDDQSFYADVYLEDGLIKQIGENLIVPGGVKTIEANGRMVIPGGIDVNTYLQKPSQGMTSADDFFQGTKAALAGGTTMIIDHVVPEPGSSLLTSFEKWHEAADTKSCCDYSLHVDITSWYDGVREELEVLVQDKGVNSFQVYMAYKDLYQMSDSQLYEAFTFLKGLGAVILVHAENGDLIAQEQKRILEMGITGPEGHALSRPEELEAEAVFRAIAIAGRINCPVYITKVMSKSAADIIALARKKGPLVFGEPIAASLGTDGTHYWSKNWAKAAAFVTSPPLSPDPTTPDYLTSLLACGDLQVTGSGHCPYSTAQKAVGKDNFTLIPEGVNGIEERMTVVWDKAVATGKMDENQFVAVTSTNAAKIFNLYPRKGRIAVGSDADVVIWDPDKMKTITAKSHKSTVEYNIFEGMECHGSPLVVISQGKIVFEDGNISVSKGMGRFIPRKPFPEHLYQRVRIRSKVFG 490
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484      

Chain B from PDB  Type:PROTEIN  Length:476
 aligned with DPYL1_MOUSE | P97427 from UniProtKB/Swiss-Prot  Length:572

    Alignment length:476
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484      
          DPYL1_MOUSE    15 DRLLIRGGRIINDDQSFYADVYLEDGLIKQIGENLIVPGGVKTIEANGRMVIPGGIDVNTYLQKPSQGMTSADDFFQGTKAALAGGTTMIIDHVVPEPGSSLLTSFEKWHEAADTKSCCDYSLHVDITSWYDGVREELEVLVQDKGVNSFQVYMAYKDLYQMSDSQLYEAFTFLKGLGAVILVHAENGDLIAQEQKRILEMGITGPEGHALSRPEELEAEAVFRAIAIAGRINCPVYITKVMSKSAADIIALARKKGPLVFGEPIAASLGTDGTHYWSKNWAKAAAFVTSPPLSPDPTTPDYLTSLLACGDLQVTGSGHCPYSTAQKAVGKDNFTLIPEGVNGIEERMTVVWDKAVATGKMDENQFVAVTSTNAAKIFNLYPRKGRIAVGSDADVVIWDPDKMKTITAKSHKSTVEYNIFEGMECHGSPLVVISQGKIVFEDGNISVSKGMGRFIPRKPFPEHLYQRVRIRSKVFG 490
               SCOP domains d1kcxb1 B:15-66,B:401-490                           d1kcxb2 B:67-400 Dihydropyrimidinase related protein-1                                                                                                                                                                                                                                                                                        d1kcxb1 B:15-66,B:401-490 Dihydropyrimidinase related protein-1                            SCOP domains
               CATH domains 1kcxB01 B:15-67,B:441-490 Urease, subunit C, domain 11kcxB02 B:68-440 Metal-dependent hydrolases                                                                                                                                                                                                                                                                                                                                          1kcxB01 B:15-67,B:441-490                          CATH domains
           Pfam domains (1) -------------------------------------------------Amidohydro_1-1kcxB01 B:64-413                                                                                                                                                                                                                                                                                                                                 ----------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------Amidohydro_1-1kcxB02 B:64-413                                                                                                                                                                                                                                                                                                                                 ----------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeee..eee....eee.eeeee..eeeeee.........eeee....eeee.eeeeee....ee..ee...hhhhhhhhhhhh.eeeeeeee......hhhhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....hhhhhhh.hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.hhhhhhh...........hhhhhhhhhhhh.............hhhhhh....hhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh................eeeeeeeeeee..................eeeeeeeeeee..eeeee..ee...............hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kcx B  15 DRLLIRGGRIINDDQSFYADVYLEDGLIKQIGENLIVPGGVKTIEANGRMVIPGGIDVNTYLQKPSQGMTSADDFFQGTKAALAGGTTMIIDHVVPEPGSSLLTSFEKWHEAADTKSCCDYSLHVDITSWYDGVREELEVLVQDKGVNSFQVYMAYKDLYQMSDSQLYEAFTFLKGLGAVILVHAENGDLIAQEQKRILEMGITGPEGHALSRPEELEAEAVFRAIAIAGRINCPVYITKVMSKSAADIIALARKKGPLVFGEPIAASLGTDGTHYWSKNWAKAAAFVTSPPLSPDPTTPDYLTSLLACGDLQVTGSGHCPYSTAQKAVGKDNFTLIPEGVNGIEERMTVVWDKAVATGKMDENQFVAVTSTNAAKIFNLYPRKGRIAVGSDADVVIWDPDKMKTITAKSHKSTVEYNIFEGMECHGSPLVVISQGKIVFEDGNISVSKGMGRFIPRKPFPEHLYQRVRIRSKVFG 490
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484      

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DPYL1_MOUSE | P97427)
molecular function
    GO:0031005    filamin binding    Interacting selectively and non-covalently with a filamin, any member of a family of high molecular mass cytoskeletal proteins that crosslink actin filaments to form networks and stress fibers. Filamins contain an amino-terminal alpha-actinin-like actin binding domain, which is followed by a rod-domain composed of 4 to 24 100-residue repetitive segments including a carboxy-terminal dimerization domain.
    GO:0016787    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.
    GO:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    GO:0051219    phosphoprotein binding    Interacting selectively and non-covalently with a phosphorylated protein.
biological process
    GO:0007411    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.
    GO:0000226    microtubule 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 microtubules and their associated proteins.
    GO:1904530    negative regulation of actin filament binding    Any process that stops, prevents or reduces the frequency, rate or extent of actin filament binding.
    GO:0010977    negative regulation of neuron projection development    Any process that decreases 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:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0071526    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0031941    filamentous actin    A two-stranded helical polymer of the protein actin.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

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