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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ERI1 EXORIBONUCLEASE 3
 
Authors :  M. Welin, M. I. Siponen, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Co A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Jo T. Karlberg, S. Kol, T. Kotenyova, E. Kouznetsova, M. Moche, T. Nyman, C. Persson, H. Schuler, P. Schutz, A. G. Thorsell, L. Tresaugues, S. Van Der Berg, E. Wahlberg, J. Weigelt, P. Nordlund, Structural Genomics Consortium
Date :  15 Sep 10  (Deposition) - 29 Sep 10  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Metal Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Welin, M. I. Siponen, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Johansson, T. Karlberg, S. Kol, T. Kotenyova, E. Kouznetsova, M. Moche, T. Nyman, C. Persson, H. Schuler, P. Schutz, A. G. Thorsell, L. Tresaugues, S. Van Der Berg, E. Wahlberg, J. Weigelt, P. Nordlund
Crystal Structure Of Human Eri1 Exoribonuclease 3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ERI1 EXORIBONUCLEASE 3
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-BSA4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: R3 PRARE
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 137-337
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PRION PROTEIN-INTERACTING PROTEIN, PRION INTERACTOR 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:150 , PHE A:151 , GLU A:152 , ASP A:312 , HOH A:2020BINDING SITE FOR RESIDUE MG A1337
2AC2SOFTWAREGLU A:152 , ALA A:153 , CYS A:155 , GLN A:163 , LEU A:203BINDING SITE FOR RESIDUE GOL A1338

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:161 -Pro A:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XRI)

(-) 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:206
 aligned with ERI3_HUMAN | O43414 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:246
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330      
           ERI3_HUMAN    91 SSYLLSRARKVLGSHLFSPCGVPEFCSISTRKLAAHGFGASMAAMVSFPPQRYHYFLVLDFEATCDKPQIHPQEIIEFPILKLNGRTMEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQCQYLGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTLAYRGFIFKQTSKP 336
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------                                       -----------RNase_T-2xr iA01 A:147-320                                                                                                                                                    ---------------- Pfam domains
         Sec.struct. author hhhhh.---------------------------------------.........eeeee..ee....-......eeeeeeeeee.....eeeeeeee.........hhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhhhh...hhhhh.eeehhhhhhhhhh.....hhhhhhhhh.........hhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xri A 130 NLYFQS---------------------------------------MSFPPQRYHYFLVLDFEATCDK-QIHPQEIIEFPILKLNGRTMEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQCQYLGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTLAYRGFIFKQTSKP 336
                                 |   -         -         -         -     | 140       150      |160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330      
                               135                                     136                  157 |                                                                                                                                                                                 
                                                                                              159
   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 2XRI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ERI3_HUMAN | O43414)
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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
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.

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