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(-) Description

Title :  STRUCTURE OF LMJPDEB1 IN COMPLEX WITH IBMX
 
Authors :  H. Wang, Z. Yan, J. Geng, S. Kunz, T. Seebeck, H. Ke
Date :  11 Sep 07  (Deposition) - 18 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Leishimaniasis, Parasite Inhibitor Selectivity, Camp Phosphodiesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Wang, Z. Yan, J. Geng, S. Kunz, T. Seebeck, H. Ke
Crystal Structure Of The Leishmania Major Phosphodiesterase Lmjpdeb1 And Insight Into The Design Of The Parasite-Selective Inhibitors.
Mol. Microbiol. V. 66 1029 2007
PubMed-ID: 17944832  |  Reference-DOI: 10.1111/J.1365-2958.2007.05976.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CLASS I PHOSPHODIESTERASE PDEB1
    Chains: A, B
    EC Number: 3.1.4.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN
    Gene: PDEB1
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1IBM2Ligand/Ion3-ISOBUTYL-1-METHYLXANTHINE
2MG2Ligand/IonMAGNESIUM ION
3ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:685 , HIS A:721 , ASP A:722 , ASP A:835 , HOH A:941 , HOH A:942BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWAREASP A:722 , HOH A:941 , HOH A:943 , HOH A:944 , HOH A:945 , HOH A:946BINDING SITE FOR RESIDUE MG A 2
3AC3SOFTWAREHIS B:685 , HIS B:721 , ASP B:722 , ASP B:835 , HOH B:942 , HOH B:943BINDING SITE FOR RESIDUE ZN B 1
4AC4SOFTWAREASP B:722 , HOH B:942 , HOH B:944 , HOH B:945 , HOH B:946 , HOH B:947BINDING SITE FOR RESIDUE MG B 2
5AC5SOFTWAREASN A:838 , PHE A:857 , GLN A:887 , PHE A:890 , HOH A:1057BINDING SITE FOR RESIDUE IBM A 3
6AC6SOFTWARETYR B:680 , ASN B:838 , GLN B:887 , PHE B:890 , HOH B:964 , HOH B:1115BINDING SITE FOR RESIDUE IBM B 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R8Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R8Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R8Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R8Q)

(-) Exons   (0, 0)

(no "Exon" information available for 2R8Q)

(-) 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:335
 aligned with Q6S996_LEIMA | Q6S996 from UniProtKB/TrEMBL  Length:940

    Alignment length:335
                                   606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926     
         Q6S996_LEIMA   597 VIAVTPEEREAVMSIDFGGAYDFTSPGFNLFEVREKYSEPMDAAAGVVYNLLWNSGLPEKFGCREQTLLNFILQCRRRYRRVPYHNFYHVVDVCQTLHTYLYTGKASELLTELECYVLLVTALVHDLDHMGVNNSFYLKTDSPLGILSSASGNNSVLEVHHCSLAIEILSDPAADVFEGLSGQDVAYAYRALIDCVLATDMAKHADALSRFTELATSGFEKDNDTHRRLVMETLIKAGDVSNVTKPFETSRMWAMAVTEEFYRQGDMEKEKGVEVLPMFDRSKNNELARGQIGFIDFVAGKFFRDIVGNLFHGMQWCVDTVNSNRAKWQEILDGR 931
               SCOP domains d2r8qa_ A: automated matches                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh..............hhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r8q A 597 VIAVTPEEREAVMSIDFGGAYDFTSPGFNLFEVREKYSEPMDAAAGVVYNLLWNSGLPEKFGCREQTLLNFILQCRRRYRRVPYHNFYHVVDVCQTLHTYLYTGKASELLTELECYVLLVTALVHDLDHMGVNNSFYLKTDSPLGILSSASGNNSVLEVHHCSLAIEILSDPAADVFEGLSGQDVAYAYRALIDCVLATDMAKHADALSRFTELATSGFEKDNDTHRRLVMETLIKAGDVSNVTKPFETSRMWAMAVTEEFYRQGDMEKEKGVEVLPMFDRSKNNELARGQIGFIDFVAGKFFRDIVGNLFHGMQWCVDTVNSNRAKWQEILDGR 931
                                   606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926     


Chain B from PDB  Type:PROTEIN  Length:335
 aligned with Q6S996_LEIMA | Q6S996 from UniProtKB/TrEMBL  Length:940

    Alignment length:335
                                   606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926     
         Q6S996_LEIMA   597 VIAVTPEEREAVMSIDFGGAYDFTSPGFNLFEVREKYSEPMDAAAGVVYNLLWNSGLPEKFGCREQTLLNFILQCRRRYRRVPYHNFYHVVDVCQTLHTYLYTGKASELLTELECYVLLVTALVHDLDHMGVNNSFYLKTDSPLGILSSASGNNSVLEVHHCSLAIEILSDPAADVFEGLSGQDVAYAYRALIDCVLATDMAKHADALSRFTELATSGFEKDNDTHRRLVMETLIKAGDVSNVTKPFETSRMWAMAVTEEFYRQGDMEKEKGVEVLPMFDRSKNNELARGQIGFIDFVAGKFFRDIVGNLFHGMQWCVDTVNSNRAKWQEILDGR 931
               SCOP domains d2r8qb_ B: automated matches                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------PDEase_I-2r8qB01 B:680-921                                                                                                                                                                                                                        ---------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------PDEase_I-2r8qB02 B:680-921                                                                                                                                                                                                                        ---------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhh..............hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r8q B 597 VIAVTPEEREAVMSIDFGGAYDFTSPGFNLFEVREKYSEPMDAAAGVVYNLLWNSGLPEKFGCREQTLLNFILQCRRRYRRVPYHNFYHVVDVCQTLHTYLYTGKASELLTELECYVLLVTALVHDLDHMGVNNSFYLKTDSPLGILSSASGNNSVLEVHHCSLAIEILSDPAADVFEGLSGQDVAYAYRALIDCVLATDMAKHADALSRFTELATSGFEKDNDTHRRLVMETLIKAGDVSNVTKPFETSRMWAMAVTEEFYRQGDMEKEKGVEVLPMFDRSKNNELARGQIGFIDFVAGKFFRDIVGNLFHGMQWCVDTVNSNRAKWQEILDGR 931
                                   606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2R8Q)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HD_PDEase (93)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q6S996_LEIMA | Q6S996)
molecular function
    GO:0004114    3',5'-cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
biological process
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.

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