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(-) Description

Title :  CRYSTAL STRUCTURE OF CYCLIC NUCLEOTIDE PHOSPHODIESTERASE OF APPR>P FROM ARABIDOPSIS THALIANA
 
Authors :  A. Hofmann, A. Zdanov, P. Genschik, W. Filipowicz, S. Ruvinov, A. Wlodawer
Date :  10 Sep 00  (Deposition) - 22 Nov 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  A,B,C  (2x)
Biol. Unit 5:  C  (2x)
Biol. Unit 6:  A (1x),B (1x)
Keywords :  Adp-Ribose 1'', 2''-Cyclic Phosphate, Appr>P, 2', 3'-Cyclic Nucleotide Phosphodiesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Hofmann, A. Zdanov, P. Genschik, S. Ruvinov, W. Filipowicz, A. Wlodawer
Structure And Mechanism Of Activity Of The Cyclic Phosphodiesterase Of Appr>P, A Product Of The Trna Splicing Reaction.
Embo J. V. 19 6207 2000
PubMed-ID: 11080166  |  Reference-DOI: 10.1093/EMBOJ/19.22.6207
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYCLIC PHOSPHODIESTERASE
    Chains: A, B, C
    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

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C
Biological Unit 4 (2x): ABC
Biological Unit 5 (2x):   C
Biological Unit 6 (1x): A (1x)B (1x) 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1SO49Ligand/IonSULFATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 4 (1, 18)
No.NameCountTypeFull Name
1SO418Ligand/IonSULFATE ION
Biological Unit 5 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 6 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:42 , THR A:44 , HIS A:119 , SER A:121 , TYR A:124 , HOH A:610 , HOH A:616 , HOH A:658 , HOH A:668BINDING SITE FOR RESIDUE SO4 A 190
2AC2SOFTWAREARG A:76 , SER A:78 , THR A:79 , GLN A:136BINDING SITE FOR RESIDUE SO4 A 191
3AC3SOFTWAREHIS B:42 , THR B:44 , HIS B:119 , SER B:121 , TYR B:124 , HOH B:211 , HOH B:222 , HOH B:258 , HOH B:265BINDING SITE FOR RESIDUE SO4 B 201
4AC4SOFTWAREARG B:76 , SER B:78 , THR B:79 , GLN B:136BINDING SITE FOR RESIDUE SO4 B 202
5AC5SOFTWARELYS A:5 , LYS A:160 , GLU A:172 , LYS B:5 , LYS B:160 , GLU B:172 , HOH B:274BINDING SITE FOR RESIDUE SO4 B 203
6AC6SOFTWAREHIS C:42 , THR C:44 , HIS C:119 , SER C:121 , TYR C:124 , HOH C:416 , HOH C:421 , HOH C:427 , HOH C:444 , HOH C:470BINDING SITE FOR RESIDUE SO4 C 401
7AC7SOFTWAREARG C:76 , SER C:78 , THR C:79 , GLN C:136BINDING SITE FOR RESIDUE SO4 C 402
8AC8SOFTWARELYS C:5 , ASP C:7 , LYS C:160 , GLU C:172BINDING SITE FOR RESIDUE SO4 C 403
9AC9SOFTWAREARG A:31 , ARG A:38 , ARG B:31 , ARG C:31 , ARG C:38BINDING SITE FOR RESIDUE SO4 A 601

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:64 -A:177
2A:104 -A:110
3B:64 -B:177
4C:64 -C:177
5C:104 -C:110

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1FSI)

(-) 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:179
 aligned with CPD_ARATH | O04147 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:183
                                                                                                                                                                                                              181  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180|  
            CPD_ARATH     1 MEEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGPRFVPHVTVAVSAYLTADEAKKMFESACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHFNCSTTTPYMPHLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLNP--   -
               SCOP domains d1fsia_ A: tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase                                                                                                             SCOP domains
               CATH domains 1fsiA00 A:1-183  [code=3.90.1140.10, no name defined]                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee...hhhhhhhhhhhhhhhh........eeeeeeeeehhhhhhhhhhhhhhhh..eeeeeeeeeeeee..eeeeeee..hhhhhhhhh.........----...eeeee....hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee...........eeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fsi A   1 MEEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGPRFVPHVTVAVSAYLTADEAKKMFESACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHFNCS----YMPHLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLNPGS 183
                                    10        20        30        40        50        60        70        80        90       100       110|    | 120       130       140       150       160       170       180   
                                                                                                                                        111  116                                                                   


Chain B from PDB  Type:PROTEIN  Length:170
 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 d1fsib_ B: tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase                                                                                                           SCOP domains
               CATH domains 1fsiB00 B:1-181  [code=3.90.1140.10, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee...hhhhhhhhhhhhhhhh........eeeeeeeeehhhhhhhhhhhhhhhh..eeeeeeeeeeeee..eeeeeee..hhhhhhhh.-----------.....eeeee....hhhhhhhhhhhhhhhh......eeeeeeeeeee...........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fsi B   1 MEEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGPRFVPHVTVAVSAYLTADEAKKMFESACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGE-----------TPYMPHLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLNP 181
                                    10        20        30        40        50        60        70        80        90       100 |       -   |   120       130       140       150       160       170       180 
                                                                                                                               102         114                                                                   


Chain C from PDB  Type:PROTEIN  Length:174
 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 d1fsic_ C: tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase                                                                                                           SCOP domains
               CATH domains 1fsiC00 C:1-181  [code=3.90.1140.10, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee...hhhhhhhhhhhhhhhh........eeeeeeeeehhhhhhhhhhhhhhhh..eeeeeeeeeeeee..eeeeeee..hhhhhhhhh..-----..--.....eeeee....hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee...........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fsi C   1 MEEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGPRFVPHVTVAVSAYLTADEAKKMFESACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHC-----CS--TPYMPHLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLNP 181
                                    10        20        30        40        50        60        70        80        90       100   |   110|  |   120       130       140       150       160       170       180 
                                                                                                                                 104   110|  |                                                                   
                                                                                                                                        111  |                                                                   
                                                                                                                                           114
   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  (1, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FSI)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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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        CPD_ARATH | O04147: 1jh6 1jh7

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