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(-) Description

Title :  STRUCTURE OF THE NEUROSPORA CRASSA PAN2 WD40 DOMAIN
 
Authors :  D. Peter, S. Jonas, E. Izaurralde, O. Weichenrieder
Date :  22 Apr 14  (Deposition) - 04 Jun 14  (Release) - 16 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Gene Regulation, Scaffold 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 - PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
    Atcc: 24698
    Chains: A, B
    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, RESIDUES 1-321
    Organism Scientific: NEUROSPORA CRASSA
    Organism Taxid: 5141
    Synonym: PAB1P-DEPENDENT POLY(A)-NUCLEASE, PAN DEADENYLATION COMPLEX CATALYTIC SUBUNIT 2, A-SPECIFIC RIBONUCLEASE SUBUNIT PAN2

 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  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:22 , ASN A:304 , LYS A:305 , HOH A:2162BINDING SITE FOR RESIDUE GOL A 400
2AC2SOFTWARESER A:16 , ARG A:58BINDING SITE FOR RESIDUE CL A 401
3AC3SOFTWARESER B:16 , ARG B:58BINDING SITE FOR RESIDUE CL B 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:14 -Pro A:15
2Tyr B:14 -Pro B:15

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CZV)

(-) 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:324
 aligned with PAN2_NEUCR | P0C581 from UniProtKB/Swiss-Prot  Length:1310

    Alignment length:324
                               1                                                                                                                                                                                                                                                                                                                                
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317    
           PAN2_NEUCR     - ---MDSRDWTQLGCVAYPSPIHPDYHAGPASTIAFDNQDELLWIGTQKGFAGSFIGRELKRFTAFRIHPETDGPLRQFLFVDKGVIFLGSRSVYMAARSGVPIWSIRHESMQDLRAMSFTSKGTSEILVAGWQNKMLVIDVNKGEVVKELPTQDQYSFLKMSRYICAATNKGTVNILDPITFTIKKQWQAHGAFINDLDTSNDFIVTCGGSHRQTHNTPAILDPYVKVFDLKNMSAMNPVPFAPLAAHVRMHPRMLTTAIVVNQAGQIHVTDLLNPSNSQVCYTQPQGVVLHFDVSRTGEGKALADNKHNTYVWGSPNKIQFTE 321
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeee...............eeee.....eeeee....eeeeee....eeeeeee..........eeee....eeee....eeee.....eeeee.......eeeeee......eeeeee...eeeeee....eeeeeee....eeeeee...eeeee....eeee......eeeee.....eeeeeee...eeeeeeeee........ee..eeeeee....ee...ee......eeee......eeeee.....eeeee......eeee.......eeeeee......eeeee...eeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4czv A  -2 PHMMDSRDWTQLGCVAYPSPIHPDYHAGPASTIAFDNQDELLWIGTQKGFAGSFIGRELKRFTAFRIHPETDGPLRQFLFVDKGVIFLGSRSVYMAARSGVPIWSIRHESMQDLRAMSFTSKGTSEILVAGWQNKMLVIDVNKGEVVKELPTQDQYSFLKMSRYICAATNKGTVNILDPITFTIKKQWQAHGAFINDLDTSNDFIVTCGGSHRQTHNTPAILDPYVKVFDLKNMSAMNPVPFAPLAAHVRMHPRMLTTAIVVNQAGQIHVTDLLNPSNSQVCYTQPQGVVLHFDVSRTGEGKALADNKHNTYVWGSPNKIQFTE 321
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317    


Chain B from PDB  Type:PROTEIN  Length:324
 aligned with PAN2_NEUCR | P0C581 from UniProtKB/Swiss-Prot  Length:1310

    Alignment length:324
                               1                                                                                                                                                                                                                                                                                                                                
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317    
           PAN2_NEUCR     - ---MDSRDWTQLGCVAYPSPIHPDYHAGPASTIAFDNQDELLWIGTQKGFAGSFIGRELKRFTAFRIHPETDGPLRQFLFVDKGVIFLGSRSVYMAARSGVPIWSIRHESMQDLRAMSFTSKGTSEILVAGWQNKMLVIDVNKGEVVKELPTQDQYSFLKMSRYICAATNKGTVNILDPITFTIKKQWQAHGAFINDLDTSNDFIVTCGGSHRQTHNTPAILDPYVKVFDLKNMSAMNPVPFAPLAAHVRMHPRMLTTAIVVNQAGQIHVTDLLNPSNSQVCYTQPQGVVLHFDVSRTGEGKALADNKHNTYVWGSPNKIQFTE 321
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeee...............eeee.....eeeee....eeeeee....eeeeeee..........eeee....eeeee..eeeee.....eeeee.......eeeeee......eeeeee...eeeeee....eeeeeee....eeeeee...eeeee...eeeee......eeeeee....eeeeeee...eeeeeeeee........ee..eeeeee....ee...ee......eeee......eeeee....eeeeee......eeee.......eeeeee......eeeee...eeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4czv B  -2 PHMMDSRDWTQLGCVAYPSPIHPDYHAGPASTIAFDNQDELLWIGTQKGFAGSFIGRELKRFTAFRIHPETDGPLRQFLFVDKGVIFLGSRSVYMAARSGVPIWSIRHESMQDLRAMSFTSKGTSEILVAGWQNKMLVIDVNKGEVVKELPTQDQYSFLKMSRYICAATNKGTVNILDPITFTIKKQWQAHGAFINDLDTSNDFIVTCGGSHRQTHNTPAILDPYVKVFDLKNMSAMNPVPFAPLAAHVRMHPRMLTTAIVVNQAGQIHVTDLLNPSNSQVCYTQPQGVVLHFDVSRTGEGKALADNKHNTYVWGSPNKIQFTE 321
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317
   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 4CZV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PAN2_NEUCR | P0C581)
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.
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:0000932    P-body    A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
    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.

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  4czv
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  PAN2_NEUCR | P0C581
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  3.1.13.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        PAN2_NEUCR | P0C581: 4czw 4czx 4czy

(-) Related Entries Specified in the PDB File

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)
4d0k COMPLEX OF CHAETOMIUM THERMOPHILUM PAN2 (WD40-CS1) WITH PAN3 (C-TERM)