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(-) Description

Title :  CRYSTAL STRUCTURE OF ARCHAEOGLOBUS FULGIDUS PELOTA REVEALS INTER-DOMAIN STRUCTURAL PLASTICITY
 
Authors :  H. H. Lee, J. Y. Jang, H. -J. Yoon, S. J. Kim, S. W. Suh
Date :  09 Aug 10  (Deposition) - 01 Sep 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Sm Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. H. Lee, J. Y. Jang, H. -J. Yoon, S. J. Kim, S. W. Suh
Crystal Structures Of Two Archaeal Pelotas Reveal Inter-Domain Structural Plasticity
Biochem. Biophys. Res. Commun. V. 399 600 2010
PubMed-ID: 20682285  |  Reference-DOI: 10.1016/J.BBRC.2010.07.121

(-) Compounds

Molecule 1 - PROTEIN PELOTA HOMOLOG
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A(+)
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3OBY)

(-) Sites  (0, 0)

(no "Site" information available for 3OBY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OBY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OBY)

(-) Sequences/Alignments

Asymmetric 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:317
 aligned with PELO_ARCFU | O29421 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:344
                                    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       340    
           PELO_ARCFU     1 MQIVEENLRDNEGEIKLIPETLDDLWHLRFIIEKGDVVFATTKRASQSSDKLRSDKEMVTVRLGIEVEKVEFHRFANRLRVSGKIVAGIEESGYHTLNITVGKELSIIKKWKPEQLERLRRAVEDSNRPEIVMLTIEEGYAVAGVLRQWGVEEIFEERMGYGKGMGDSRKEFFGEVAAKLESFDFKYLIVAGPGFAKNDFLDFLKERYPEMAKNAVVVDVSSVGSRGFIEILKRRVVDKIVGEVRLAEEAEYIDRLLEGIAKGERVAYGLDEVREAHNYRAIEVLLVADEFLLEEREKWDVDGLLREVEESGGKVVIMSTEFEPGKRLMSLGGIAALLRFNVKG 344
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeeee..hhhhhhhhhhhh....eeee...---------------....eeeeeeeeee......eeeeeeeee.----.eeeeee.....eeeeee.hhhhhhhhhhhhh......eeeeeee..eeeeeeee..eeeeeeeee.--------...hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeehhhhhhhhhh...eeeeeeehhhhhhhh...hhhhhhhhhhhh..eeeee...hhhhhhhhhh..eeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oby A   1 MQIVEENLRDNEGEIKLIPETLDDLWHLRFIIEKGDVVFATTK---------------VTVRLGIEVEKVEFHRFANRLRVSGKIVAG----GYHTLNITVGKELSIIKKWKPEQLERLRRAVEDSNRPEIVMLTIEEGYAVAGVLRQWGVEEIFEERM--------SRKEFFGEVAAKLESFDFKYLIVAGPGFAKNDFLDFLKERYPEMAKNAVVVDVSSVGSRGFIEILKRRVVDKIVGEVRLAEEAEYIDRLLEGIAKGERVAYGLDEVREAHNYRAIEVLLVADEFLLEEREKWDVDGLLREVEESGGKVVIMSTEFEPGKRLMSLGGIAALLRFNVKG 344
                                    10        20        30        40  |      -        60        70        80       | -  |    100       110       120       130       140       150        |-       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    
                                                                     43              59                           88   93                                                               159      168                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:316
 aligned with PELO_ARCFU | O29421 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:344
                                    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       340    
           PELO_ARCFU     1 MQIVEENLRDNEGEIKLIPETLDDLWHLRFIIEKGDVVFATTKRASQSSDKLRSDKEMVTVRLGIEVEKVEFHRFANRLRVSGKIVAGIEESGYHTLNITVGKELSIIKKWKPEQLERLRRAVEDSNRPEIVMLTIEEGYAVAGVLRQWGVEEIFEERMGYGKGMGDSRKEFFGEVAAKLESFDFKYLIVAGPGFAKNDFLDFLKERYPEMAKNAVVVDVSSVGSRGFIEILKRRVVDKIVGEVRLAEEAEYIDRLLEGIAKGERVAYGLDEVREAHNYRAIEVLLVADEFLLEEREKWDVDGLLREVEESGGKVVIMSTEFEPGKRLMSLGGIAALLRFNVKG 344
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) eRF1_1-3obyB05 B:1-125                                                                                                       ----eRF1_2-3obyB03 B:130-243                                                                                          --eRF1_3-3obyB01 B:246-342                                                                         -- Pfam domains (1)
           Pfam domains (2) eRF1_1-3obyB06 B:1-125                                                                                                       ----eRF1_2-3obyB04 B:130-243                                                                                          --eRF1_3-3obyB02 B:246-342                                                                         -- Pfam domains (2)
         Sec.struct. author .eeeee.....eeeeeee..hhhhhhhhhhhh....eeee...----------------...eeeeeeeeee......eeeeeee..----..eeeeee.....eeeeee.hhhhhhhhhhhhhh.....eeeeeee..eeeeeee....ee...eee...--------..hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhhheee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhh..eeeeeeehhhhhhhh...hhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oby B   1 MQIVEENLRDNEGEIKLIPETLDDLWHLRFIIEKGDVVFATTK----------------TVRLGIEVEKVEFHRFANRLRVSGKIVA----SGYHTLNITVGKELSIIKKWKPEQLERLRRAVEDSNRPEIVMLTIEEGYAVAGVLRQWGVEEIFEERMGY--------KEFFGEVAAKLESFDFKYLIVAGPGFAKNDFLDFLKERYPEMAKNAVVVDVSSVGSRGFIEILKRRVVDKIVGEVRLAEEAEYIDRLLEGIAKGERVAYGLDEVREAHNYRAIEVLLVADEFLLEEREKWDVDGLLREVEESGGKVVIMSTEFEPGKRLMSLGGIAALLRFNVKG 344
                                    10        20        30        40  |      -        60        70        80      |  - |     100       110       120       130       140       150       160|      170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340    
                                                                     43               60                         87   92                                                                  161      170
   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 3OBY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 6)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PELO_ARCFU | O29421)
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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 Related Entries

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

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(-) Related Entries Specified in the PDB File

3obw SSO PELOTA