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(-) Description

Title :  CRYSTAL STRUCTURE OF THE THERMOPLASMA ACIDOPHILUM PELOTA PROTEIN
 
Authors :  H. H. Lee, Y. S. Kim, K. H. Kim, I. H. Heo, S. K. Kim, O. Kim, S. W. Suh
Date :  03 Jul 07  (Deposition) - 09 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Pelota, Dom34, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. H. Lee, Y. S. Kim, K. H. Kim, I. Heo, S. K. Kim, O. Kim, H. K. Kim, J. Y. Yoon, H. S. Kim, D. J. Kim, S. J. Lee, H. J. Yoon, S. J. Kim, B. G. Lee, H. K. Song, V. N. Kim, C. M. Park, S. W. Suh
Structural And Functional Insights Into Dom34, A Key Component Of No-Go Mrna Decay
Mol. Cell V. 27 938 2007
PubMed-ID: 17889667  |  Reference-DOI: 10.1016/J.MOLCEL.2007.07.019
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CELL DIVISION PROTEIN PELOTA RELATED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A(+)
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 2303
    Synonym: PELOTA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2QI2)

(-) Sites  (0, 0)

(no "Site" information available for 2QI2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QI2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QI2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QI2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QI2)

(-) Exons   (0, 0)

(no "Exon" information available for 2QI2)

(-) 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:312
 aligned with PELO_THEAC | Q9HJ74 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:338
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330        
           PELO_THEAC     1 MRILEEDLKNSTYRIRIESLDDLWYLRNILSEGDEVSAITFRRVEESADVQRSRERERIPITIRLKVEKIEFQDFDNRLRILGTVIEGPEDTKGKHQSITVTVDSEISITKEWDDQHIDLLKEATDEKYVTVYTAVAMDEDEAQIFLIHPYGIQQVGTVYSGRSGKYAEGNYSEASYFDQIVNALKNYSNSIIILGPGFARDRFARYCAQRGVNVIGSFPANRTDSGAVYEFITSADGAKLLSNERIARDKEIVDEFLVAVKKDMGVYGRDQTESALQMGALSDLIITDEMFRTEDGRRSLSIAQTVGTRIHIVSVSNDPGQIVKKFGGFAGILRYRV 338
               SCOP domains d2qi2a1 A:1-126 Cell division protein pel             ota                                                                     d2qi2a2 A:127-243 Cell division protein p    elota                                                                   d2qi2a3 A:244-338 Cell division protein pelota                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains eRF1_1-2qi2A03 A:1-127                                                                                                         ----eRF1_2-2qi2A02 A:132-244                                                                                         --eRF1_3-2qi2A01 A:247-338                                                                     Pfam domains
         Sec.struct. author .eeeeee....eeeee...hhhhhhhhhhh....eeeeee.-------------..eeeeeeeeeee.......eeeeeee..---------...eeeeee....eeeee...hhhhhhhhhhhhhhhhhh.eeeeee...eeeeeee....eeeeeeee.hhhhhh----.hhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhh.......ee....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhh..eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qi2 A   1 MRILEEDLKNSTYRIRIESLDDLWYLRNILSEGDEVSAITF-------------ERERIPITIRLKVEKIEFQDFDNRLRILG---------KGKHQSITVTVDSEISITKEWDDQHIDLLKEATDEKYVTVYTAVAMDEDEAQIFLIHPYGIQQVGTVYSGRSGKY----YSEASYFDQIVNALKNYSNSIIILGPGFARDRFARYCAQRGVNVIGSFPANRTDSGAVYEFITSADGAKLLSNERIARDKEIVDEFLVAVKKDMGVYGRDQTESALQMGALSDLIITDEMFRTEDGRRSLSIAQTVGTRIHIVSVSNDPGQIVKKFGGFAGILRYRV 338
                                    10        20        30        40|        -    |   60        70        80  |      -  |    100       110       120       130       140       150       160      |  - |     180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330        
                                                                   41            55                          83        93                                                                       167  172
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QI2)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: RNA_ribose_bind (78)
(-)
Clan: S11_L18p (67)
(-)
Clan: no clan defined [family: eRF1_1] (6)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PELO_THEAC | Q9HJ74)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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.
biological process
    GO:0071025    RNA surveillance    The set of processes involved in identifying and degrading defective or aberrant RNAs.
    GO:0070966    nuclear-transcribed mRNA catabolic process, no-go decay    The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA with stalls in translation elongation.
    GO:0070481    nuclear-transcribed mRNA catabolic process, non-stop decay    The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that is lacking a stop codon.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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