Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF DROSOPHILA MELANOGASTER PAN3 PSEUDOKINASE
 
Authors :  M. Christie, A. Boland, E. Huntzinger, O. Weichenrieder, E. Izaurrald
Date :  03 Jul 13  (Deposition) - 21 Aug 13  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.60
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: PNYC-NPM
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PSEUDOKINSE DOMAIN, COILED COIL, CTERMINAL KNOB, RESIDUES 349-790
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    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  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1AN22Ligand/IonAMP PHOSPHORAMIDATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:392 , ALA B:395 , GLN B:396 , THR B:408 , ARG B:423 , VAL B:451 , ASP B:472 , TYR B:473 , HIS B:474 , SER B:477 , GLN B:478 , THR B:479 , THR B:552BINDING SITE FOR RESIDUE AN2 B1788
2AC2SOFTWAREPRO A:393 , PRO A:394 , ALA A:395 , GLN A:396 , THR A:408 , ARG A:423 , VAL A:451 , ASP A:472 , HIS A:474 , SER A:477 , GLN A:478 , THR A:479BINDING SITE FOR RESIDUE AN2 A1788

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:392 -Pro A:393
2Glu B:392 -Pro B:393

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4BWP)

(-) 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:386
 aligned with PAN3_DROME | Q95RR8 from UniProtKB/Swiss-Prot  Length:790

    Alignment length:409
                                   388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778         
           PAN3_DROME   379 PLEVENYHALYPLEPPAQPLHAKLTFPATTYRATHNTTGYKYCLRRIHGFRLQSTKCMTLVEMWKKLQHTNVVQLREVFTTKAFGDNSLVLVYDYHPGSQTLLAKYFTPAPETNGYTDPFQGEARPFSHKSNMQRTSNGPLLPEATIWSIIMQLTAGLKAIHHAGLACKVLDPTKIIVTGKRVRFSSCCISDITQFDPNASNPLALVNMHQQDDLTALGRLVLALACRCLQSVQRDNVQSSIDMVTRNYSTDLRNFIVYLFTTNNRRSVTDLMPMIGARFYTQLDALQSKIDMQEDELAKEMENGRLYRILVKLNSINERPDFNLDCTWSETGDRYMLKLFRDYLFHSVTEDGRPWLDHAHIVQCLNKLDAGSIERVQLMSRDEQSVLIVSYAELKNCLENAFSELMSS 787
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.......ee...ee.eeeeeeee.....eeeeeeee......hhhhhhhhhhhh........eeeeeee......eeeeeee.....eehhhhhh....-----------------------.........hhhhhhhhhhhhhhhhhhhh............eeee..eeee....hhhhh............hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh..hhhhhhhhhhh...........hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhh............hhhhhhhhhhhhh....eeeee......eeeeehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bwp A 379 PLEVENYHALYPLEPPAQPLHAKLTFPATTYRATHNTTGYKYCLRRIHGFRLQSTKCMTLVEMWKKLQHTNVVQLREVFTTKAFGDNSLVLVYDYHPGSQTLLAKYFTPAP-----------------------RTSNGPLLPEATIWSIIMQLTAGLKAIHHAGLACKVLDPTKIIVTGKRVRFSSCCISDITQFDPNASNPLALVNMHQQDDLTALGRLVLALACRCLQSVQRDNVQSSIDMVTRNYSTDLRNFIVYLFTTNNRRSVTDLMPMIGARFYTQLDALQSKIDMQEDELAKEMENGRLYRILVKLNSINERPDFNLDCTWSETGDRYMLKLFRDYLFHSVTEDGRPWLDHAHIVQCLNKLDAGSIERVQLMSRDEQSVLIVSYAELKNCLENAFSELMSS 787
                                   388       398       408       418       428       438       448       458       468       478       488|        -         -    |  518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778         
                                                                                                                                        489                     513                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:372
 aligned with PAN3_DROME | Q95RR8 from UniProtKB/Swiss-Prot  Length:790

    Alignment length:409
                                   388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778         
           PAN3_DROME   379 PLEVENYHALYPLEPPAQPLHAKLTFPATTYRATHNTTGYKYCLRRIHGFRLQSTKCMTLVEMWKKLQHTNVVQLREVFTTKAFGDNSLVLVYDYHPGSQTLLAKYFTPAPETNGYTDPFQGEARPFSHKSNMQRTSNGPLLPEATIWSIIMQLTAGLKAIHHAGLACKVLDPTKIIVTGKRVRFSSCCISDITQFDPNASNPLALVNMHQQDDLTALGRLVLALACRCLQSVQRDNVQSSIDMVTRNYSTDLRNFIVYLFTTNNRRSVTDLMPMIGARFYTQLDALQSKIDMQEDELAKEMENGRLYRILVKLNSINERPDFNLDCTWSETGDRYMLKLFRDYLFHSVTEDGRPWLDHAHIVQCLNKLDAGSIERVQLMSRDEQSVLIVSYAELKNCLENAFSELMSS 787
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eeeeee...............eeeeeeee.....eeeeeeee.......hhhhhhhhhhh........eeeeeee......eeeeeee.....eehhhhh...--------------------------........hhhhhhhhhhhhhhhhhhhh............eeee..eeee..hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh..hhhhhhhhhhh...........hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..-----------.hhhhhhhhhhhhh............hhhhhhhhhhhhh....eeeee......eeeeehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bwp B 379 PLEVENYHALYPLEPPAQPLHAKLTFPATTYRATHNTTGYKYCLRRIHGFRLQSTKCMTLVEMWKKLQHTNVVQLREVFTTKAFGDNSLVLVYDYHPGSQTLLAKYFTP--------------------------TSNGPLLPEATIWSIIMQLTAGLKAIHHAGLACKVLDPTKIIVTGKRVRFSSCCISDITQFDPNASNPLALVNMHQQDDLTALGRLVLALACRCLQSVQRDNVQSSIDMVTRNYSTDLRNFIVYLFTTNNRRSVTDLMPMIGARFYTQLDALQSKIDMQEDELAKEMENGRLYRILVKLNSINERP-----------GDRYMLKLFRDYLFHSVTEDGRPWLDHAHIVQCLNKLDAGSIERVQLMSRDEQSVLIVSYAELKNCLENAFSELMSS 787
                                   388       398       408       418       428       438       448       458       468       478        |-         -         -     | 518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698|        -  |    718       728       738       748       758       768       778         
                                                                                                                                      487                        514                                                                                                                                                                                      699         711
   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 4BWP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PAN3_DROME | Q95RR8)
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.
    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).
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
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.
    GO:0010606    positive regulation of cytoplasmic mRNA processing body assembly    Any process that increases the rate, frequency, or extent of the aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    AN2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:392 - Pro A:393   [ RasMol ]  
    Glu B:392 - Pro B:393   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4bwp
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PAN3_DROME | Q95RR8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PAN3_DROME | Q95RR8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4BWP)

(-) Related Entries Specified in the PDB File

4bwk STRUCTURE OF NEUROSPORA CRASSA PAN3 PSEUDOKINASE
4bwx STRUCTURE OF NEUROSPORA CRASSA PAN3 PSEUDOKINASE MUTANT