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(-) Description

Title :  STRUCTURE OF THE SACCHAROMYCES CEREVISIAE PAN2 PSEUDOUBIQUITIN-HYDROLASE
 
Authors :  I. B. Schaefer, E. Conti
Date :  27 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 :  Ubiquitin Carboxyl-Terminal Hydrolase-Like Domain, Uch, Pan3, Inactive, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. B. Schafer, M. Rode, F. Bonneau, S. Schussler, E. Conti
The Structure Of The Pan2-Pan3 Core Complex Reveals Cross-Talk Between Deadenylase And Pseudokinase.
Nat. Struct. Mol. Biol. V. 21 591 2014
PubMed-ID: 24880344  |  Reference-DOI: 10.1038/NSMB.2834

(-) Compounds

Molecule 1 - PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN2
    Chains: A, B
    EC Number: 3.1.13.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEC-A-3C-ZTA
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 416-870
    Gene: PAN2, YGL094C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: PAB1P-DEPENDENT POLY(A)-NUCLEASE, PAN DEADENYLATION COMPLEX CATALYTIC SUBUNIT 2

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:660 , HIS A:662 , CYS A:713 , CYS A:716BINDING SITE FOR RESIDUE ZN A 901
2AC2SOFTWARECYS B:660 , ASP B:661 , HIS B:662 , CYS B:713 , CYS B:716BINDING SITE FOR RESIDUE ZN B 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q8G)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:640 -Asn A:641
2Lys B:615 -Arg B:616

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q8G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q8G)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q8G)

(-) 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:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhh.......hhhhh..............hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhheeeeeeee........eeeee..eee......hhhhhhhhheeeeeeeee......eeeeeeeeee.....eeeeee..hhhhhhhhhhh......eeeeeee..eeeee.hhhhh....eeeeeeeeeeeeeee.....eeeeeeeeeee....eeeeeeee..eeeeehhhhhhh.....eeeeeeeeee.hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q8g A 461 TSDIQTYTSINKYEVPPAYSRLPLTFDFTPFNNTEYSGLDPDVDNHYTNAIIQLYRFIPEMFNFVVGCLKDTTLLTDLGYLFDMMERSHGKICSSSNFQASLKSLTSIKRNMPQKFNRFLLSQLIKEEAQTVNHNITLNQCFGLETEIRTECSCDHYDTTVKLLPSLSISGINQNILPYIEYAMKNVTQKNSICPTCGKTETITQECTVKNLPSVLSLELSLLDTEFSNIRSSKNWLTSEFYGSIIKNKAVLRSTASELKGTSHIFKYELNGYVAKITDNNNETRLVTYVKKYNPKENCFKWLMFNDYLVVEITEEEALKMTYPWKTPEIIIYCDAEELRKPFF 863
                                   470       480    || 498       508       518       528       538||     552       562       572     ||616       626       636       646       656       666       676  ||   699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859    
                                                  485|                                          539|                               578|                                                               679|                                                                                                                                                                          
                                                   494                                           544                                613                                                                693                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhh......hhhhh....hhhhh..............hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhheeeeeeee........eeeee..eee....hhhhhhhhheeeeeeeee......eeeeeeeeee.....eeeeee..hhhhhhhhhh.......eeeeee....eeee.hhhhh....eeeeeeeeeeeeeee.....eeeeeeeeeee....eeeeeeee..eeeeehhhhhh......eeeeeeeeee.hhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q8g B 460 ETSDIQTYTSINKYEVPPAYSRLPLTSGRFGTDNFDFTPFNNTEYSGLDPDVDNHYTNAIIQLYRFIPEMFNFVVGCLKDENFETTLLTDLGYLFDMMERSHGKICSSSNFQASLKSLTKRNMPQKFNRFLLSQLIKEEAQTVNHNITLNQCFGLETEIRTECSCDHYDTTVKLLPSLSISGQNILPYIEYAMKNVTQKNSICPTCGKTETITQECTVKNLPSVLSLELSLLDTEFSNIRSSKNWLTSEFYGSIIKNKAVLRSTASELKGTSHIFKYELNGYVAKITDNNNETRLVTYVKKYNPKENCFKWLMFNDYLVVEITEEEALKMTYPWKTPEIIIYCDAEELRKPFF 863
                                   469       479       489       499       509       519       529       539       549       559       569       615       625       635       645       655       665       675 ||    700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860   
                                                                                                                                                578|                                                           677|                                                                                                                                                                          
                                                                                                                                                 615                                                            693
   Legend:   → Mismatch (orange background)
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  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 4Q8G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q8G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q8G)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

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  4q8g
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  PAN2_YEAST | P53010
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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_YEAST | P53010: 4q8h 4xr7

(-) Related Entries Specified in the PDB File

4q8h STRUCTURE OF THE SACCHAROMYCES CEREVISIAE PAN2 PSEUDOUBIQUITIN-HYDROLASE-RNASE MODULE
4q8j STRUCTURE OF THE SACCHAROMYCES CEREVISIAE PAN2-PAN3 CORE COMPLEX