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(-) Description

Title :  SEMI-REDUCED CYCLIC NUCLEOTIDE PHOSPHODIESTERASE FROM ARABIDOPSIS THALIANA
 
Authors :  A. Hofmann, M. Grella, I. Botos, W. Filipowicz, A. Wlodawer
Date :  27 Jun 01  (Deposition) - 06 Feb 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (3x)
Keywords :  Adp-Ribose 1'', 2''-Cyclic Phosphate, Rna Processing, 2', 3'-Cyclic Nucleotide Phosphodiesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Hofmann, M. Grella, I. Botos, W. Filipowicz, A. Wlodawer
Crystal Structures Of The Semireduced And Inhibitor-Bound Forms Of Cyclic Nucleotide Phosphodiesterase From Arabidopsis Thaliana.
J. Biol. Chem. V. 277 1419 2002
PubMed-ID: 11694509  |  Reference-DOI: 10.1074/JBC.M107889200

(-) Compounds

Molecule 1 - CYCLIC PHOSPHODIESTERASE
    Chains: A, B
    EC Number: 3.1.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11D+
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 12)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:42 , THR A:44 , HIS A:119 , SER A:121 , TYR A:124 , HOH A:302 , HOH A:303 , HOH A:304 , HOH A:305 , HOH A:308 , HOH A:413BINDING SITE FOR RESIDUE SO4 A 211
2AC2SOFTWAREARG A:31 , ARG A:38 , HOH A:393BINDING SITE FOR RESIDUE SO4 A 212
3AC3SOFTWAREHIS B:42 , THR B:44 , HIS B:119 , SER B:121 , TYR B:124 , HOH B:502 , HOH B:503 , HOH B:504 , HOH B:505 , HOH B:508 , HOH B:662BINDING SITE FOR RESIDUE SO4 B 221
4AC4SOFTWAREARG B:31 , ARG B:38 , HOH B:518BINDING SITE FOR RESIDUE SO4 B 222

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:64 -A:177
2B:64 -B:177

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JH6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JH6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JH6)

(-) Exons   (0, 0)

(no "Exon" information available for 1JH6)

(-) 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:181
 aligned with CPD_ARATH | O04147 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
            CPD_ARATH     1 MEEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGPRFVPHVTVAVSAYLTADEAKKMFESACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHFNCSTTTPYMPHLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLNP 181
               SCOP domains d1jh6a_ A: tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase                                                                                                           SCOP domains
               CATH domains 1jh6A00 A:1-181  [code=3.90.1140.10, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee...hhhhhhhhhhhhhhhhh.......eeeeeeeeehhhhhhhhhhhhhhh...eeeeeeeeeeeee..eeeeeee..hhhhhhhhhhhhhhh..........eeeee....hhhhhhhhhhhhhhhh......eeeeeeeeeee...........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jh6 A   1 MEEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGPRFVPHVTVAVSAYLTADEAKKMFESACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHFNCSTTTPYMPHLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLNP 181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 


Chain B from PDB  Type:PROTEIN  Length:181
 aligned with CPD_ARATH | O04147 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
            CPD_ARATH     1 MEEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGPRFVPHVTVAVSAYLTADEAKKMFESACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHFNCSTTTPYMPHLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLNP 181
               SCOP domains d1jh6b_ B: tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase                                                                                                           SCOP domains
               CATH domains 1jh6B00 B:1-181  [code=3.90.1140.10, no name defined]                                                                                                                                 CATH domains
           Pfam domains (1) CPDase-1jh6B01 B:1-179                                                                                                                                                             -- Pfam domains (1)
           Pfam domains (2) CPDase-1jh6B02 B:1-179                                                                                                                                                             -- Pfam domains (2)
         Sec.struct. author ........eeeeeee...hhhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhhhhhh..eeeeeeeeeeeee..eeeeeee..hhhhhhhhhhhhhhh..........eeeee....hhhhhhhhhhhhhhhh......eeeeeeeeeee...........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jh6 B   1 MEEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGPRFVPHVTVAVSAYLTADEAKKMFESACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHFNCSTTTPYMPHLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLNP 181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: 2H (3)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CPD_ARATH | O04147)
molecular function
    GO:0004112    cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: a nucleoside cyclic phosphate + H2O = a nucleoside phosphate.
    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.
biological process
    GO:0006388    tRNA splicing, via endonucleolytic cleavage and ligation    Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.
cellular component
    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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  1jh6
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  3.1.4.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        CPD_ARATH | O04147: 1fsi 1jh7

(-) Related Entries Specified in the PDB File

1fsi OXIDISED CYCLIC NUCLEOTIDE PHOSPHODIESTERASE FROM ARABIDOPSIS THALIANA
1jh7 SEMI-REDUCED INHIBITOR-BOUND CYCLIC NUCLEOTIDE PHOSPHODIESTERASE FROM ARABIDOPSIS THALIANA