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(-) Description

Title :  STRUCTURE OF THE C-TERMINAL SEC63 UNIT OF YEAST BRR2, P41212 FORM
 
Authors :  V. Pena, R. L. Hrmann, M. C. Wahl
Date :  09 Aug 09  (Deposition) - 25 Aug 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A
Keywords :  Atpase, Rna Helicase, Rnpase, Rna Unwindase, Molecular Modeling, Pre- Mrna Splicing, Spliceosome Catalytic Activation, U5-200K Protein/Brr2, Atp-Binding, Helicase, Hydrolase, Mrna Processing, Mrna Splicing, Nucleotide-Binding, Nucleus, Phosphoprotein, Spliceosome (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Pena, S. M. Jovin, P. Fabrizio, J. Orlowski, J. M. Bujnicki, R. L. Hrmann, M. C. Wahl
Common Design Principles In The Spliceosomal Rna Helicase Brr2 And In The Hel308 Dna Helicase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PRE-MRNA-SPLICING HELICASE BRR2
    ChainsA
    EC Number3.6.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM-11
    Expression System StrainROSETTA2 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSEC63 UNIT (UNP RESIDUES 1839-2163)
    GeneBRR2, RSS1, SNU246, SYGP-ORF66, YER172C
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:120 , HOH A:122 , HOH A:177 , HOH A:314 , LEU A:1939 , THR A:1974 , ASP A:1978 , GLN A:1981 , TRP A:2143 , ASP A:2153BINDING SITE FOR RESIDUE PG4 A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IM2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IM2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IM2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IM2)

(-) Exons   (0, 0)

(no "Exon" information available for 3IM2)

(-) 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:320
 aligned with BRR2_YEAST | P32639 from UniProtKB/Swiss-Prot  Length:2163

    Alignment length:320
                                  1853      1863      1873      1883      1893      1903      1913      1923      1933      1943      1953      1963      1973      1983      1993      2003      2013      2023      2033      2043      2053      2063      2073      2083      2093      2103      2113      2123      2133      2143      2153      2163
          BRR2_YEAST   1844 ISTLSNGLIASHYGVSFFTIQSFVSSLSNTSTLKNMLYVLSTAVEFESVPLRKGDRALLVKLSKRLPLRFPEHTSSGSVSFKVFLLLQAYFSRLELPVDFQNDLKDILEKVVPLINVVVDILSANGYLNATTAMDLAQMLIQGVWDVDNPLRQIPHFNNKILEKCKEINVETVYDIMALEDEERDEILTLTDSQLAQVAAFVNNYPNVELTYSLNNSDSLISGVKQKITIQLTRDVEPENLQVTSEKYPFDKLESWWLVLGEVSKKELYAIKKVTLNKETQQYELEFDTPTSGKHNLTIWCVCDSYLDADKELSFEINVK 2163
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.............hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeee......ee...eeeeeeeee......................eeeeeeehhhheeeeeeee.....eeeeeeeee....eeeeeeeeeee.......eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3im2 A 1844 ISTLSNGLIASHYGVSFFTIQSFVSSLSNTSTLKNMLYVLSTAVEFESVPLRKGDRALLVKLSKRLPLRFPEHTSSGSVSFKVFLLLQAYFSRLELPVDFQNDLKDILEKVVPLINVVVDILSANGYLNATTAMDLAQMLIQGVWDVDNPLRQIPHFNNKILEKCKEINVETVYDIMALEDEERDEILTLTDSQLAQVAAFVNNYPNVELTYSLNNSDSLISGVKQKITIQLTRDVEPENLQVTSEKYPFDKLESWWLVLGEVSKKELYAIKKVTLNKETQQYELEFDTPTSGKHNLTIWCVCDSYLDADKELSFEINVK 2163
                                  1853      1863      1873      1883      1893      1903      1913      1923      1933      1943      1953      1963      1973      1983      1993      2003      2013      2023      2033      2043      2053      2063      2073      2083      2093      2103      2113      2123      2133      2143      2153      2163

   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 3IM2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IM2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IM2)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BRR2_YEAST | P32639)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004004    ATP-dependent RNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    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:0000388    spliceosome conformational change to release U4 (or U4atac) and U1 (or U11)    Rearrangement of the pre-catalytic spliceosome containing U4 (or U4atac) and U1 (or U11) snRNPs to unpair U4 (or U4atac) from U6 (or U6atac) and release it from the spliceosomal complex along with U1 (or U11).
cellular component
    GO:0046540    U4/U6 x U5 tri-snRNP complex    A ribonucleoprotein complex formed by the association of the U4/U6 and U5 small nuclear ribonucleoproteins.
    GO:0005682    U5 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U5.
    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.
    GO:0005681    spliceosomal complex    Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BRR2_YEAST | P326393hib 3im1 3jcm 4bgd 5dca 5gan 5gao 5gap 5gm6 5lj5 5lqw 5m52 5m5p

(-) Related Entries Specified in the PDB File

3im1 SAME PROTEIN, OTHER CRYSTAL FORM