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(-) Description

Title :  COMPLEX OF CHAETOMIUM THERMOPHILUM PAN2 (WD40-CS1) WITH PAN3 (C-TERM)
 
Authors :  S. Jonas, E. Izaurralde, O. Weichenrieder
Date :  28 Apr 14  (Deposition) - 04 Jun 14  (Release) - 16 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Gene Regulation, Wd40 Domain, C-Terminal Knob Domain, Deadenylation, Mrna Decay, Pan2-Pan3 Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Jonas, M. Christie, D. Peter, D. Bhandari, B. Loh, E. Huntzinger, O. Weichenrieder, E. Izaurralde
An Asymmetric Pan3 Dimer Recruits A Single Pan2 Exonuclease To Mediate Mrna Deadenylation And Decay.
Nat. Struct. Mol. Biol. V. 21 599 2014
PubMed-ID: 24880343  |  Reference-DOI: 10.1038/NSMB.2837

(-) Compounds

Molecule 1 - A-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
    Chains: A
    EC Number: 3.1.13.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETMCN (PNYC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector Type: PLASMID
    Fragment: WD40 DOMAIN AND CS1, RESIDUES 1-457
    Organism Scientific: CHAETOMIUM THERMOPHILUM
    Organism Taxid: 209285
    Strain: DSM 1495
    Synonym: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2, PAB1P-DEPENDENT POLY(A)-NUCLEASE, PAN DEADENYLATION COMPLEX CATALYTIC SUBUNIT 2
 
Molecule 2 - PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3-LIKE PROTEIN
    Chains: B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETMCN (PNEA)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector Type: PLASMID
    Fragment: C-TERM, RESIDUES 448-555
    Organism Scientific: CHAETOMIUM THERMOPHILUM
    Organism Taxid: 209285
    Strain: DSM 1495
    Synonym: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3, PAB1P-DEPENDENT POLY(A)-NUCLEASE, PAN DEADENYLATION COMPLEX SUBUNIT 3, A-SPECIFIC RIBONUCLEASE SUBUNIT PAN3

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4D0K)

(-) Sites  (0, 0)

(no "Site" information available for 4D0K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D0K)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:13 -Pro A:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D0K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D0K)

(-) Exons   (0, 0)

(no "Exon" information available for 4D0K)

(-) 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:329
 aligned with G0SAK8_CHATD | G0SAK8 from UniProtKB/TrEMBL  Length:1170

    Alignment length:345
                                    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     
         G0SAK8_CHATD     1 MDADWDEVTRIAYPAPGTNDFPRPATAVAFDPIAELLWAGFDRGRVCSFYGRDLTRYTAFKIQPASEGPVRQFLFHDKGVIVLGTRSVHMAMRRGPALWNIRHENMKDLRCMSFTSKGTQEIIVAGWQDTMLVIDVLKGDIIKQIPAQHHYSIMKKSRYICAATKTGSVDLIDPLSFKIVRSWQAHASYINDMDAQNDFIVTCGGSLKQQAAQTYMLDPYVNVFDLKNMASMKPMPFPPLAAHVRLHPRMLTTAIVTSQHGQMHVVDIMNPNSSTVRYANISSYVKLFEIAPSGEALVIGDADCNIHLWGSPTKIHFTDMAIPIELPEPEEPAPVLDWSIETPLS 345
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee......--......eeee.....eeeee....eeeeee....eeeeeee..........eeeee..eeeee...eeeee.....eeeeee......eeeeee......eeeeee...eeeeee....eeeeeee....eeeeee...eeeee...eeeee......eeeeee....eeeeeeee..eeeeeee.--------.....eeeeee....eee..ee......eeee......eeeee....eeeeee.......eeee......eeeeee......eeeee...eeeeee..................-----......-..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d0k A   1 MDADWDEVTRIAYPAPGT--FPRPATAVAFDPIAELLWAGFDRGRVCSFYGRDLTRYTAFKIQPASEGPVRQFLFHDKGVIVLGTRSVHMAMRRGPALWNIRHENMKDLRCMSFTSKGTQEIIVAGWQDTMLVIDVLKGDIIKQIPAQHHYSIMKKSRYICAATKTGSVDLIDPLSFKIVRSWQAHASYINDMDAQNDFIVTCGGS--------YMLDPYVNVFDLKNMASMKPMPFPPLAAHVRLHPRMLTTAIVTSQHGQMHVVDIMNPNSSTVRYANISSYVKLFEIAPSGEALVIGDADCNIHLWGSPTKIHFTDMAIPIELPE-----PVLDWS-ETPLS 345
                                    10       | -|       30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     |   -    |  220       230       240       250       260       270       280       290       300       310       320       | -   |    |-|    
                                            18 21                                                                                                                                                                                      206      215                                                                                                              328   334  339 |    
                                                                                                                                                                                                                                                                                                                                                                              341    


Chain B from PDB  Type:PROTEIN  Length:105
 aligned with G0S0Y3_CHATD | G0S0Y3 from UniProtKB/TrEMBL  Length:566

    Alignment length:105
                                   460       470       480       490       500       510       520       530       540       550     
         G0S0Y3_CHATD   451 NGRIARSLMKLLTILERGDYDGVPSWSETGDRYQLKLFRDYVFHRVDADGKPNLSIGHMLTCMSKLEAGVDENILLTSRDNETVFVLSYRELRQMYDRAFNELVK 555
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..................hhhhhhhhhhh............hhhhhhhhhhhhh....eeeee......eeeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 4d0k B 451 NGRIARSLMKLLTILERGDYDGVPSWSETGDRYQLKLFRDYVFHRVDADGKPNLSIGHMLTCMSKLEAGVDENILLTSRDNETVFVLSYRELRQMYDRAFNELVK 555
                                   460       470       480       490       500       510       520       530       540       550     


Chain C from PDB  Type:PROTEIN  Length:109
 aligned with G0S0Y3_CHATD | G0S0Y3 from UniProtKB/TrEMBL  Length:566

    Alignment length:109
                                   456       466       476       486       496       506       516       526       536       546         
         G0S0Y3_CHATD   447 REVENGRIARSLMKLLTILERGDYDGVPSWSETGDRYQLKLFRDYVFHRVDADGKPNLSIGHMLTCMSKLEAGVDENILLTSRDNETVFVLSYRELRQMYDRAFNELVK 555
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh...............hhhhhhhhhhhhhh............hhhhhhhhhhhhh....eeeee......eeeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 4d0k C 447 LEVENGRIARSLMKLLTILERGDYDGVPSWSETGDRYQLKLFRDYVFHRVDADGKPNLSIGHMLTCMSKLEAGVDENILLTSRDNETVFVLSYRELRQMYDRAFNELVK 555
                                   456       466       476       486       496       506       516       526       536       546
   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 4D0K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D0K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D0K)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (G0SAK8_CHATD | G0SAK8)
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: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:0004535    poly(A)-specific ribonuclease activity    Catalysis of the exonucleolytic cleavage of poly(A) to 5'-AMP.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    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:0000288    nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay    A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.
    GO:0000289    nuclear-transcribed mRNA poly(A) tail shortening    Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
    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:0031251    PAN complex    A complex that possesses poly(A)-specific ribonuclease activity; catalyzes the message-specific shortening of mRNA poly(A) tails. Contains at least two subunits, known as Pan2p and Pan3p in Saccharomyces.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B,C   (G0S0Y3_CHATD | G0S0Y3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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.

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    Tyr A:13 - Pro A:14   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        G0S0Y3_CHATD | G0S0Y3: 4cyi 4cyj
        G0SAK8_CHATD | G0SAK8: 4cyj

(-) Related Entries Specified in the PDB File

4czv STRUCTURE OF THE NEUROSPORA CRASSA PAN2 WD40 DOMAIN
4czw STRUCTURE OF THE NEUROSPORA CRASSA PAN2 CATALYTIC UNIT (PROTEASE AND NUCLEASE DOMAIN)
4czx COMPLEX OF NEUROSPORA CRASSA PAN2 (WD40) WITH PAN3 (C -TERM)
4czy COMPLEX OF NEUROSPORA CRASSA PAN2 (WD40-CS1) WITH PAN3 (PSEUDOKINASE AND C-TERM)