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(-) Description

Title :  STRUCTURE OF THE NEUROSPORA CRASSA PAN2 CATALYTIC UNIT (PROTEASE AND NUCLEASE DOMAIN)
 
Authors :  M. Christie, E. Izaurralde, O. Weichenrieder
Date :  22 Apr 14  (Deposition) - 04 Jun 14  (Release) - 16 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Gene Regulation, Deed Exoribonuclease, Ubiquitin Specific Protease, 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: UBIQUITIN SPECIFIC PROTEASE DOMAIN AND EXORIBONUCLEASE DOMAIN, RESIDUES 456-1100
    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

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE
2ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:525 , CYS A:530 , CYS A:535 , CYS A:538BINDING SITE FOR RESIDUE ZN A3094
2AC2SOFTWARECYS A:645 , CYS A:648 , CYS A:700 , CYS A:703BINDING SITE FOR RESIDUE ZN A3095

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:533 -Pro A:534
2Ser A:791 -Pro A:792

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1USP_3PS50235 Ubiquitin specific protease (USP) domain profile.PAN2_NEUCR494-850  1A:494-850

(-) Exons   (0, 0)

(no "Exon" information available for 4CZW)

(-) 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:609
 aligned with PAN2_NEUCR | P0C581 from UniProtKB/Swiss-Prot  Length:1310

    Alignment length:638
                                   465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075      1085        
          PAN2_NEUCR    456 DHWSLRPEAPPEYRICEIKYSKFGVDDFDFGFFNNTPYPGLENNITNSYANSLLQVMHYTPLLRNMALQHAATACLADPCLLCELGYVFDMLQKGEGPSCHATNMLRALNHTSNASVSGVLEDIAKDKNPSTLVKNLTMFLFDKISQDYKGTPPISTELERTLFKLNQPPNPLDLVKRLLETDARYQIKCMHCQHVSPRTATTFVNKLCYPAAKPNIRGMKAQRITFSQVLKAGLENEAVNKGYCTKCQRYQNLDQRKIIFNIPAVLALCTEITTAEHRKLWSTPGWLPEEIGIIVDQGHVYCYEGDDLKLHLNRGIHNITVYSLVGTVVNVETKSPQKSHLVATVNVGRAEPESKDQDRWHLFNDFSVRGISKVEALTFNAAWKMPVVVMFQVKAANHRFNMDWKTRLDTSVLFRDNNPHALKTYELLDRETEIPGPDTVIAIDTEFIRLKEREIHIDEDGKSKTIRPISHAIARASVVRGQGSREGVAFIDDYIHIKETIVDYLTEWSGITPTDLDPINSQRNLVSPKTAYKKLWVLVNLGCKFLGHGLSQDFRVINIQVPRNQVIDTSIIFMKPPSQRKISLAFLAWYLLKEDIQQNTHDSIEDAQTALKLYRKYEEFMANGSFHDVLEALYKKG 1093
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................................ee.........hhhhhhhh..hhhhhhhhhhh.........hhhhhhhhhhhhhh....ee..hhhhhhh....................hhhhhhhhhhhhhhhhhhhh........hhhhhh........hhhhhhhhh..eeeeeeee.....eeeeee....ee.....----------....hhhhhhhhh..eeeeeeee....eeeeeeeeeeeee...eeeee.....hhhhhhh........eeeeeee..eeeeeehhhhhhhhh.--...eeeeeeeeeeeeee....eeeeeeeee.............eeeee..eeee..hhhh.......eeeeeeeeee.........hhhh....hhhh.........................eeeeeeeeeee.-----------------.eeeeeeeeeee........eeeeeee.....eee..hhhh...hhhh.......eee.hhhhhhhhhhhhh...eeee..hhhhhhhh........eeehhhh...........hhhhhhhh...........hhhhhhhhhhhhhhhhhhhh...hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------USP_3  PDB: A:494-850 UniProt: 494-850                                                                                                                                                                                                                                                                                                                               --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4czw A  456 DHWSLRPEAPPEYRICEIKYSKFGVDDFDFGFFNNTPYPGLENNITNSYANSLLQVmHYTPLLRNmALQHAATACLADPCLLCELGYVFDmLQKGEGPSCHATNmLRALNHTSNASVSGVLEDIAKDKNPSTLVKNLTmFLFDKISQDYKGTPPISTELERTLFKLNQPPNPLDLVKRLLETDARYQIKCmHCQHVSPRTATTFVNKLCYPA----------QRITFSQVLKAGLENEAVNKGYCTKCQRYQNLDQRKIIFNIPAVLALCTEITTAEHRKLWSTPGWLPEEIGIIVDQGHVYCYEGDDLKLHLNR--HNITVYSLVGTVVNVETKSPQKSHLVATVNVGRAEPESKDQDRWHLFNDFSVRGISKVEALTFNAAWKmPVVVmFQVKAANHRFNmDWKTRLDTSVLFRDNNPHALKTYELLDRETEIPGPDTVIAIDTEFIRLK-----------------ISHAIARASVVRGQGSREGVAFIDDYIHIKETIVDYLTEWSGITPTDLDPINSQRNLVSPKTAYKKLWVLVNLGCKFLGHGLSQDFRVINIQVPRNQVIDTSIIFmKPPSQRKISLAFLAWYLLKEDIQQNTHDSIEDAQTALKLYRKYEEFmANGSFHDVLEALYKKG 1093
                                   465       475       485       495       505      |515     | 525       535       545|      555    |  565       575       585       595       605       615       625       635       645|      655       665 |       -  |    685       695       705       715       725       735       745       755       765    |  775       785       795       805       815       825       835     | 845|      855  |    865       875       885       895       905 |       -       925       935       945       955       965       975       985       995      1005      1015      1025    | 1035      1045      1055      1065      1075 |    1085        
                                                                                  512-MSE  521-MSE                  546-MSE       560-MSE                           594-MSE                                             646-MSE              667        678                                                                                         770  |                                                                 841-MSE|         858-MSE                                          907               925                                                                                                     1030-MSE                                       1077-MSE            
                                                                                                                                                                                                                                                                                                                                                       773                                                                      846-MSE
   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 4CZW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological 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.

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  4czw
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4czv STRUCTURE OF THE NEUROSPORA CRASSA PAN2 WD40 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)