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(-) Description

Title :  CRYSTALLOGRAPHIC STRUCTURE OF THE NUCLEASE DOMAIN OF 3'HEXO, A DEDDH FAMILY MEMBER, BOUND TO RAMP
 
Authors :  Y. Cheng, D. Patel
Date :  04 Jun 04  (Deposition) - 30 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym./Biol. Unit :  A
Keywords :  Nuclease Domain, Hydrolase, Nuclease, Exonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Cheng, D. Patel
Crystallographic Structure Of The Nuclease Domain Of 3'Hexo, A Deddh Family Member, Bound To Ramp
J. Mol. Biol. V. 343 305 2004
PubMed-ID: 15451662  |  Reference-DOI: 10.1016/J.JMB.2004.08.055

(-) Compounds

Molecule 1 - 3'-5' EXONUCLEASE ERI1
    ChainsA
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGBO
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentNUCLEASE DOMAIN, RESIDUES 122-321
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsRAMP
    Other Details - SourceSYNTHETIC GENE
    SynonymERI-1 HOMOLOG, PROTEIN 3'HEXO

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:134 , ASP A:234 , MG A:1001 , AMP A:1002 , HOH A:2020 , HOH A:2242BINDING SITE FOR RESIDUE MG A1000
2AC2SOFTWAREASP A:134 , GLU A:136 , ASP A:298 , MG A:1000 , AMP A:1002BINDING SITE FOR RESIDUE MG A1001
3AC3SOFTWAREASP A:134 , PHE A:135 , GLU A:136 , ALA A:137 , THR A:138 , CYS A:139 , PHE A:185 , ASP A:234 , PHE A:238 , HIS A:293 , ASP A:298 , MG A:1000 , MG A:1001 , HOH A:2020 , HOH A:2035 , HOH A:2365 , HOH A:2366 , HOH A:2367 , HOH A:2370BINDING SITE FOR RESIDUE AMP A1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W0H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W0H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W0H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W0H)

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000002502632bENSE00001019501chr8:8860314-8860681368ERI1_HUMAN1-36360--
1.4bENST000002502634bENSE00001019499chr8:8865480-8865658179ERI1_HUMAN37-96600--
1.6aENST000002502636aENSE00001019497chr8:8869052-8869262211ERI1_HUMAN96-166711A:123-16644
1.7aENST000002502637aENSE00001019504chr8:8873832-887391584ERI1_HUMAN167-194281A:167-19428
1.8bENST000002502638bENSE00000924781chr8:8875807-8875916110ERI1_HUMAN195-231371A:195-23137
1.9aENST000002502639aENSE00000924782chr8:8877860-8877974115ERI1_HUMAN231-269391A:231-26939
1.10bENST0000025026310bENSE00001533120chr8:8887302-88908483547ERI1_HUMAN270-349801A:270-32253

(-) 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:200
 aligned with ERI1_HUMAN | Q8IV48 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:200
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322
           ERI1_HUMAN   123 ADSYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDWMKLKELGTKYKYSLLTDGSWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLGMDYDGRPHCGLDDSKNIARIAVRMLQDGCELRINEKM 322
               SCOP domains d1w0ha_ A: Exonuclease ERI1                                                                                                                                                                              SCOP domains
               CATH domains 1w0hA00 A:123-321  [code=3.30.420.10, no name defined]                                                                                                                                                 - CATH domains
               Pfam domains --------RNase_T-1w0hA01 A:131-306                                                                                                                                                       ---------------- Pfam domains
         Sec.struct. author ......eeee...ee.............eeeeeeeeee.....eeeeeeee.........hhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhh...hhhh.eeeehhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh.......ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6a  PDB: A:123-166 UniProt: 96-166   Exon 1.7a  PDB: A:167-194   Exon 1.8b  PDB: A:195-231            --------------------------------------Exon 1.10b  PDB: A:270-322 UniProt: 270-349           Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------Exon 1.9a  PDB: A:231-269              ----------------------------------------------------- Transcript 1 (2)
                 1w0h A 123 ADSYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDWmKLKELGTKYKYSLLTDGSWDmSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTImLEKLGmDYDGRPHCGLDDSKNIARIAVRmLQDGCELRINEKm 322
                                   132       142       152       162       172       182       192       202       212 |     222       232  |    242       252       262       272       282   |   292       302      |312       322
                                                                                                                     214-MSE              235-MSE                                      280-MSE |                    309-MSE      322-MSE
                                                                                                                                                                                             286-MSE                                

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: RNase_H (288)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ERI1_HUMAN | Q8IV48)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0071207    histone pre-mRNA stem-loop binding    Interacting selectively and non-covalently with a conserved stem-loop structure found in histone pre-mRNAs.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
biological process
    GO:0000467    exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)    Exonucleolytic digestion of a pre-rRNA molecule to generate the mature 3'-end of a 5.8S rRNA molecule derived from an originally tricistronic pre-rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0071044    histone mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of histone messenger RNA (mRNA).
    GO:0031125    rRNA 3'-end processing    Any process involved in forming the mature 3' end of an rRNA molecule.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0071204    histone pre-mRNA 3'end processing complex    A ribonucleoprotein that binds to specific sites in, and is required for cleavage of, the 3'-end of histone pre-mRNAs. The complex contains the U7 snRNP and additional proteins, including the stem-loop binding protein (SLBP) and the exonuclease 3'hExo/Eri-1.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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
        ERI1_HUMAN | Q8IV481zbh 1zbu 4l8r 4qoz

(-) Related Entries Specified in the PDB File

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