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(-) Description

Title :  NMR STRUCTURE OF RCL IN COMPLEX WITH GMP
 
Authors :  A. Padilla, Y. Yang, G. Labesse, C. Zhang, P. A. Kaminski
Date :  02 Jul 09  (Deposition) - 20 Oct 09  (Release) - 02 Jan 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
NMR Structure *:  A,B  (1x)
Keywords :  Protein, Gmp, N-Glycosidase, Nucleus, Phosphoprotein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Yang, A. Padilla, C. Zhang, G. Labesse, P. A. Kaminski
Structural Characterization Of The Mammalian Deoxynucleotid N-Hydrolase Rcl And Its Stabilizing Interactions With Two Inhibitors
J. Mol. Biol. V. 394 435 2009
PubMed-ID: 19822152  |  Reference-DOI: 10.1016/J.JMB.2009.10.004

(-) Compounds

Molecule 1 - C-MYC-RESPONSIVE PROTEIN RCL
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBLI5
    Expression System Taxid562
    Expression System VectorPET24A
    Expression System Vector TypeVECTOR
    FragmentRESIDUES IN UNP 11-151
    GeneRCL
    MutationYES
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  12
NMR Structure (10x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
15GP2Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
NMR Structure * (1, 2)
No.NameCountTypeFull Name
15GP2Ligand/IonGUANOSINE-5'-MONOPHOSPHATE

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:13 , CYS A:15 , GLY A:16 , SER A:17 , ILE A:18 , ARG A:19 , TYR A:28 , THR A:43 , HIS A:45 , ILE A:65 , GLN A:68 , ALA A:69 , TRP A:72 , GLY A:89 , GLU A:93 , SER B:117 , ALA B:118 , MET B:119BINDING SITE FOR RESIDUE 5GP A 187
2AC2SOFTWARESER A:117 , ALA A:118 , MET A:119 , TYR B:13 , CYS B:15 , GLY B:16 , SER B:17 , ILE B:18 , ARG B:19 , TYR B:28 , THR B:43 , HIS B:45 , ILE B:65 , GLN B:68 , ALA B:69 , TRP B:72 , GLY B:89 , GLU B:93BINDING SITE FOR RESIDUE 5GP B 187

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KLH)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2KLH)

(-) Sequences/Alignments

NMR Structure
   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:152
 aligned with DNPH1_RAT | O35820 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
            DNPH1_RAT     1 MAASGEQAPCSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEHVADAELEPLGEEAAGGDQFIHEQDLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEAYLPQKTASSS 159
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-------eeeee........hhhhhhhhhhhhhhhhee..hhhhh............hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh..eeeee........hhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2klh A   8 MRR-------SVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEHVADAELEPLGEEAAGGDQFIHEQALNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEAYLVEHHHHHH 159
                              |      -|       20        30        40        50        60        70        80        90       100       110       120       130       140       150         
                             10      11                                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with DNPH1_RAT | O35820 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
            DNPH1_RAT     1 MAASGEQAPCSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEHVADAELEPLGEEAAGGDQFIHEQDLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEAYLPQKTASSS 159
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-------eeeee........hhhhhhhhhhhhhhhhee..hhhhh............hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh..eeeee........hhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2klh B   8 MRR-------SVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEHVADAELEPLGEEAAGGDQFIHEQALNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEAYLVEHHHHHH 159
                              |      -|       20        30        40        50        60        70        80        90       100       110       120       130       140       150         
                             10      11                                                                                                                                                    

   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 2KLH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KLH)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A,B   (DNPH1_RAT | O35820)
molecular function
    GO:0070694    deoxyribonucleoside 5'-monophosphate N-glycosidase activity    Catalysis of the reaction: a deoxyribonucleoside 5'-monophosphate + H2O = deoxyribose 5-monophosphate + a purine or pyrimidine base.
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0016799    hydrolase activity, hydrolyzing N-glycosyl compounds    Catalysis of the hydrolysis of any N-glycosyl bond.
    GO:0050144    nucleoside deoxyribosyltransferase activity    Catalysis of the reaction: 2-deoxy-D-ribosyl-base1 + base2 = 2-deoxy-D-ribosyl-base2 + base1.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0009159    deoxyribonucleoside monophosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with phosphate on the sugar.
    GO:0030855    epithelial cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0009117    nucleotide metabolic process    The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A 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.
    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

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DNPH1_RAT | O358202khz 4fyh 4fyi 4fyk 4kxl 4kxm 4kxn 4p5d

(-) Related Entries Specified in the PDB File

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