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(-) Description

Title :  COMPLEX OF NEUROSPORA CRASSA PAN2 (WD40) WITH PAN3 (C-TERM)
 
Authors :  S. Jonas, E. Izaurralde, O. Weichenrieder
Date :  22 Apr 14  (Deposition) - 04 Jun 14  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
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 - PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
    Atcc: 24698
    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, 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
 
Molecule 2 - PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3
    Atcc: 24698
    Chains: B
    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 538-656
    Organism Scientific: NEUROSPORA CRASSA
    Organism Taxid: 5141
    Synonym: PAB1P-DEPENDENT POLY(A)-NUCLEASE, PAN DEADENYLATION COMPLEX SUBUNIT 3, A-SPECIFIC RIBONUCLEASE SUBUNIT PAN3

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:129 , SER A:154 , PHE A:191 , ILE A:192 , ASN A:193 , ARG A:210 , GLN A:211 , THR A:212 , HIS A:213 , ALA A:217 , HOH A:2123 , HOH A:2159 , HOH A:2178BINDING SITE FOR RESIDUE MES A 400
2AC2SOFTWAREARG A:88 , ARG A:104BINDING SITE FOR RESIDUE PO4 A 401
3AC3SOFTWARETRP A:129 , ASN A:167 , LYS A:168 , ARG A:210 , HOH A:2161 , HOH A:2238BINDING SITE FOR RESIDUE GOL A 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CZX)

(-) 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...eeeee......eeeeee....eeeeeee...eeeeeee..............eeeeee....ee...ee......eeee......eeeee....eeeeee......eeeee......eeeeee......eeeee...eeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4czx 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:103
 aligned with PAN3_NEUCR | Q7SDP4 from UniProtKB/Swiss-Prot  Length:656

    Alignment length:107
                                   548       558       568       578       588       598       608       618       628       638       
           PAN3_NEUCR   539 LENGRIARLMFKLSVVNERGDSCGVHNWSETGERLLLKLFRDYVFHQVDADGKARLDTNHYLNCLSKLDASSEEQILLTSRDNATVFVVSYRSIRQMLDRAYGELGK 645
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.....----..hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhh.....eeeee......eeeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 4czx B 539 LENGRIARLMFKLSVVNERGD----HNWSETGERLLLKLFRDYVFHQVDADGKARLDTNHYLNCLSKLDASSEEQILLTSRDNATVFVVSYRSIRQMLDRAYGELGK 645
                                   548       558|    | 568       578       588       598       608       618       628       638       
                                              559  564
   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 4CZX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 21)

Asymmetric Unit(hide GO term definitions)
Chain A   (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.

Chain B   (PAN3_NEUCR | Q7SDP4)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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.
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.

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  4czx
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  PAN2_NEUCR | P0C581
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  PAN3_NEUCR | Q7SDP4
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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: 4czv 4czw 4czy
        PAN3_NEUCR | Q7SDP4: 4bwk 4bwx 4czy

(-) 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)
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)