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(-) Description

Title :  STRUCTURE OF NEUROSPORA CRASSA PAN3 PSEUDOKINASE MUTANT
 
Authors :  M. Christie, A. Boland, E. Huntzinger, O. Weichenrieder, E. Izaurrald
Date :  04 Jul 13  (Deposition) - 21 Aug 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gene Regulation, Deadenylase, Pan2, Mirna, Mrna Decay (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Christie, A. Boland, E. Huntzinger, O. Weichenrieder, E. Izaurralde
Structure Of The Pan3 Pseudokinase Reveals The Basis For Interactions With The Pan2 Deadenylase And The Gw182 Proteins
Mol. Cell V. 51 360 2013
PubMed-ID: 23932717  |  Reference-DOI: 10.1016/J.MOLCEL.2013.07.011

(-) Compounds

Molecule 1 - PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNEA-NPM
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PSEUDOKINASE DOMAIN, COILED COIL, CTERMINAL KNOB DOMAIN, RESIDUES 234-656
    Mutation: YES
    Organism Scientific: NEUROSPORA CRASSA
    Organism Taxid: 5141
    Synonym: PAB1P-DEPENDENT POLY(A)-NUCLEASE, PAB-DEPENDENT POLYA-SPECIFIC RIBONUCLEASE SUBUNIT PAN-3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1AGS2Ligand/IonPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:271 , SER A:285 , AGS A:1647BINDING SITE FOR RESIDUE MG A1648
2AC2SOFTWARELEU A:270 , ASP A:271 , THR A:275 , SER A:285 , MET A:287 , ARG A:302 , HIS A:354 , SER A:357 , GLU A:358 , THR A:359 , SER A:412 , LYS A:413 , ILE A:415 , MG A:1648BINDING SITE FOR RESIDUE AGS A1647
3AC3SOFTWARELEU B:270 , THR B:272 , CYS B:280 , SER B:285 , MET B:287 , ALA B:300 , ARG B:302 , VAL B:331 , ASP B:352 , PHE B:353 , HIS B:354 , SER B:357 , GLU B:358 , THR B:359 , LYS B:413 , MG B:1648BINDING SITE FOR RESIDUE AGS B1647
4AC4SOFTWAREASP B:271 , SER B:285 , AGS B:1647BINDING SITE FOR RESIDUE MG B1648

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BWX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4BWX)

(-) 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:395
 aligned with PAN3_NEUCR | Q7SDP4 from UniProtKB/Swiss-Prot  Length:656

    Alignment length:413
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643   
           PAN3_NEUCR   234 IPKDRRENLQKKLFHMQQLLPNSGLPNLDRWHSLFPLDTKATRNSTCFGYPSWMYKAQNNKNGRHFALRRIEGYRLTNEKAILNVTKEWKKIINANIVTVHEAFTTEFFGDSSLIFVYDFHPLSETLYDHHFPPNNSHNRLRNTNKIPENLLWSYVCQIANALLAIHNAKLAARCLELSKIIWENNRIRLAACSILDVLHHDSPNRKTIEELQQEDFVKFGRIILALATNTPTLNFNNIDAALATIVPRYSTQLRGVLEWLIKPSAPGETKTVETLLGGITTHLANFANFVMQESDEKEFHLMRELENGRIARLMFKLSVVNERGDSCGVHNWSETGERLLLKLFRDYVFHQVDADGKARLDTNHYLNCLSKLDASSEEQILLTSRDNATVFVVSYRSIRQMLDRAYGELGKE 646
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.............eeeeee...............eeeeeeee.....eeeeeeee.............hhhh..........eeeeeee......eeeeeee.....eehhhhh...----------....hhhhhhhhhhhhhhhhhhh.............eeee..eeee.....hhhh.........hhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhh..........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...--------......hhhhhhhhhhhh............hhhhhhhhhhhh.....eeeee......eeeeehhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bwx A 234 IPKDRRENLQKKLFHMQQLLPNSGLPNLDRWHSLFPLDTKATRNSTCFGYPSWMYKAQNNKNGRHFALRRIEGYRLTNEKAILNVTKEWKKIINANIVTVHEAFTTEFFGDSSLIFVYDFHPLSETLYDHHFPP----------NKIPENLLWSYVCQIANALLAIHNAKLAARCLELSKIIWENNRIRLAACSILDVLHHDSPNRKTIEELQQEDFVKFGRIILALATNTPTLNFNNIDAALATIVPRYSTQLRGVLEWLIKPSAPGETKTVETLMPMIGARFANFANFVMQESDEKEFHLMRELENGRIARLMFKLSVVNER--------WSETGERLLLKLFRDYVFHQVDADGKARLDTNHYLNCLSKLDASSEEQILLTSRDNATVFVVSYRSIRQMLDRAYGELGKE 646
                                   243       253       263       273       283       293       303       313       323       333       343       353       363   |     -    |  383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553   |     -  |    573       583       593       603       613       623       633       643   
                                                                                                                                                               367        378                                                                                                                                                                                557      566                                                                                


Chain B from PDB  Type:PROTEIN  Length:397
 aligned with PAN3_NEUCR | Q7SDP4 from UniProtKB/Swiss-Prot  Length:656

    Alignment length:413
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643   
           PAN3_NEUCR   234 IPKDRRENLQKKLFHMQQLLPNSGLPNLDRWHSLFPLDTKATRNSTCFGYPSWMYKAQNNKNGRHFALRRIEGYRLTNEKAILNVTKEWKKIINANIVTVHEAFTTEFFGDSSLIFVYDFHPLSETLYDHHFPPNNSHNRLRNTNKIPENLLWSYVCQIANALLAIHNAKLAARCLELSKIIWENNRIRLAACSILDVLHHDSPNRKTIEELQQEDFVKFGRIILALATNTPTLNFNNIDAALATIVPRYSTQLRGVLEWLIKPSAPGETKTVETLLGGITTHLANFANFVMQESDEKEFHLMRELENGRIARLMFKLSVVNERGDSCGVHNWSETGERLLLKLFRDYVFHQVDADGKARLDTNHYLNCLSKLDASSEEQILLTSRDNATVFVVSYRSIRQMLDRAYGELGKE 646
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.............eeeeee...............eeeeeeee.....eeeeeeee.......hhhhhhhhhh..........eeeeeee......eeeeeee.....eehhhhh.......------....hhhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhh.........hhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhh..........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...----------....hhhhhhhhhhhh............hhhhhhhhhhhh.....eeeee......eeeeehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bwx B 234 IPKDRRENLQKKLFHMQQLLPNSGLPNLDRWHSLFPLDTKATRNSTCFGYPSWMYKAQNNKNGRHFALRRIEGYRLTNEKAILNVTKEWKKIINANIVTVHEAFTTEFFGDSSLIFVYDFHPLSETLYDHHFPPNNSH------NKIPENLLWSYVCQIANALLAIHNAKLAARCLELSKIIWENNRIRLAACSILDVLHHDSPNRKTIEELQQEDFVKFGRIILALATNTPTLNFNNIDAALATIVPRYSTQLRGVLEWLIKPSAPGETKTVETLMPMIGARFANFANFVMQESDEKEFHLMRELENGRIARLMFKLSVVNER----------ETGERLLLKLFRDYVFHQVDADGKARLDTNHYLNCLSKLDASSEEQILLTSRDNATVFVVSYRSIRQMLDRAYGELGKE 646
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       | -    |  383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553   |     -    |  573       583       593       603       613       623       633       643   
                                                                                                                                                                   371    378                                                                                                                                                                                557        568
   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 4BWX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,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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 Related Entries

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

UniProtKB/Swiss-Prot
        PAN3_NEUCR | Q7SDP4: 4bwk 4czx 4czy

(-) Related Entries Specified in the PDB File

4bwk STRUCTURE OF NEUROSPORA CRASSA PAN3 PSEUDOKINASE
4bwp STRUCTURE OF DROSOPHILA MELANOGASTER PAN3 PSEUDOKINASE