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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN CNOT6L NUCLEASE DOMAIN IN COMPLEX WITH AMP
 
Authors :  H. Wang, M. Morita, W. Yang, M. Bartlam, T. Yamamoto, Z. Rao
Date :  12 Jun 10  (Deposition) - 28 Jul 10  (Release) - 28 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Amp Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Wang, M. Morita, X. Yang, T. Suzuki, W. Yang, J. Wang, K. Ito, Q. Wang, C. Zhao, M. Bartlam, T. Yamamoto, Z. Rao
Crystal Structure Of The Human Cnot6L Nuclease Domain Reveals Strict Poly(A) Substrate Specificity.
Embo J. 2010
PubMed-ID: 20628353  |  Reference-DOI: 10.1038/EMBOJ.2010.152

(-) Compounds

Molecule 1 - CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 6-LIKE
    ChainsA
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P-1
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentNUCLEASE DOMAIN (UNP RESIDUES 158-555)
    GeneCNOT6L, CCR4B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCNOT6L, CARBON CATABOLITE REPRESSOR PROTEIN 4 HOMOLOG B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:240 , HIS A:360 , TRP A:363 , PRO A:365 , LYS A:371 , ASP A:410 , ASN A:412 , ASN A:479 , PHE A:484 , HIS A:529 , HOH A:592 , HOH A:614BINDING SITE FOR RESIDUE AMP A 556
2AC2SOFTWARETRP A:174 , SER A:188 , THR A:190 , ILE A:271 , MET A:272 , SER A:273 , GLU A:276 , GLN A:535 , HOH A:558BINDING SITE FOR RESIDUE AMP A 557

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Cys A:520 -Pro A:521

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NGN)

(-) 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:324
 aligned with CNO6L_HUMAN | Q96LI5 from UniProtKB/Swiss-Prot  Length:555

    Alignment length:372
                                   178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538  
          CNO6L_HUMAN   169 LPPRPWITLKERDQILPSASFTVMCYNVLCDKYATRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYDGFFSPKSRAKIMSEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQVAMANSDGSEAMLNRVMTKDNIGVAVVLEVHKELFGAGMKPIHAADKQLLIVANAHMHWDPEYSDVKLIQTMMFVSEVKNILEKASSRPGSPTADPNSIPLVLCADLNSLPDSGVVEYLSNGGVADNHKDFKELRYNECLMNFSCNGKNGSSEGRITHGFQLKSAYENNLMPYTNYTFDFKGVIDYIFYSKTHMNVLGVLGPLDPQWLVENNITGCPHPHIPSDHFSLLTQLELHP 540
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------    ------Exo_endo_phos-3ngnA01 A:192-529                                                                                                                                                                                                                                                                                                                   ----------- Pfam domains
         Sec.struct. author .....eee.....----.eeeeeeeee..hhhhh........hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhh..eeeeeee.......hhhhhhhheeeeeeee...eeeeeeeeeehhhhhhh....hhhhhhhh.....eeeeeeeee.hhhh-----------..eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh------------...eeeeee......hhhhhhhhh.ee...hhhhh.---------------------.ee....eee..........ee....ee..eeeeee...eeeeeee...hhhhhhhh................eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ngn A 169 LPPRPWITLKERD----SASFTVMCYNVLCDKYATRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYDGFFSPKSRAKIMSEQERKHVDGCAIFFKTEKFTLVQKHTVEFNQVAMANSDGSEAMLNRVMTKDNIGVAVVLEVHKELF-----------KQLLIVANAHMHWDPEYSDVKLIQTMMFVSEVKNILEKA------------SIPLVLCADLNSLPDSGVVEYLSNGGVADNHKDFKE---------------------RITHGFQLKSAYENNLMPYTNYTFDFKGVIDYIFYSKTHMNVLGVLGPLDPQWLVENNITGCPHPHIPSDHFSLLTQLELHP 540
                                   178  |    188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338|        -  |    358       368       378       388|        -   |   408       418       428        |-         -         -|      468       478       488       498       508       518       528       538  
                                      181  186                                                                                                                                                      339         351                                   389          402                                437                   459                                                                                 

   Legend:   → Mismatch (orange background)
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  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 3NGN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CNO6L_HUMAN | Q96LI5)
molecular function
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0004535    poly(A)-specific ribonuclease activity    Catalysis of the exonucleolytic cleavage of poly(A) to 5'-AMP.
    GO:0005515    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).
biological process
    GO:0006977    DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0061157    mRNA destabilization    Any process that decreases the stability of an mRNA molecule, making it more vulnerable to degradative processes. Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0000288    nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay    A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.
    GO:0000289    nuclear-transcribed mRNA poly(A) tail shortening    Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0010606    positive regulation of cytoplasmic mRNA processing body assembly    Any process that increases the rate, frequency, or extent of the aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0030014    CCR4-NOT complex    The evolutionarily conserved CCR4-NOT complex is involved in several aspects of mRNA metabolism, including repression and activation of mRNA initiation, control of mRNA elongation, and the deadenylation and subsequent degradation of mRNA. In Saccharomyces the CCR4-NOT complex comprises a core complex of 9 proteins (Ccr4p, Caf1p, Caf40p, Caf130p, Not1p, Not2p, Not3p, Not4p, and Not5p), Caf4p, Caf16p, and several less well characterized proteins.
    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

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

UniProtKB/Swiss-Prot
        CNO6L_HUMAN | Q96LI53ngo 3ngq 5dv2 5dv4

(-) Related Entries Specified in the PDB File

3ngo 3ngq