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(-) Description

Title :  CRYSTAL STRUCTURE OF POLYNEURIDINE ALDEHYDE ESTERASE MUTANT (H244A)
 
Authors :  L. Yang, M. Hill, S. Panjikar, M. Wang, J. Stoeckigt
Date :  08 Apr 09  (Deposition) - 21 Apr 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Keywords :  Alkaloid Metabolism, Monoterpenoid Indole Alkaloids, Pnae, Hydrolase, Serine Esterase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Yang, M. Hill, M. Wang, S. Panjikar, J. Stockigt
Structural Basis And Enzymatic Mechanism Of The Biosynthesis Of C9- From C10-Monoterpenoid Indole Alkaloids.
Angew. Chem. Int. Ed. Engl. V. 48 5211 2009
PubMed-ID: 19496101  |  Reference-DOI: 10.1002/ANIE.200900150

(-) Compounds

Molecule 1 - POLYNEURIDINE ALDEHYDE ESTERASE
    Chains: A, B, C, D, E
    EC Number: 3.1.1.78
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-2
    Expression System Strain: M15PREP4
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: SERPENTWOOD
    Organism Scientific: RAUVOLFIA SERPENTINA
    Organism Taxid: 4060

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): A    
Biological Unit 2 (1x):  B   
Biological Unit 3 (1x):   C  
Biological Unit 4 (1x):    D 
Biological Unit 5 (1x):     E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2WFM)

(-) Sites  (0, 0)

(no "Site" information available for 2WFM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WFM)

(-) 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:255
 aligned with PNAE_RAUSE | Q9SE93 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:255
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258     
           PNAE_RAUSE     9 QQKHFVLVHGGCLGAWIWYKLKPLLESAGHKVTAVDLSAAGINPRRLDEIHTFRDYSEPLMEVMASIPPDEKVVLLGHSFGGMSLGLAMETYPEKISVAVFMSAMMPDPNHSLTYPFEKYNEKCPADMMLDSQFSTYGNPENPGMSMILGPQFMALKMFQNCSVEDLELAKMLTRPGSLFFQDLAKAKKFSTERYGSVKRAYIFCNEDKSFPVEFQKWFVESVGADKVKEIKEADHMGMLSQPREVCKCLLDISD 263
               SCOP domains d2wfma_ A: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2wfmA00 A:9-263  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh..eeeee..........hhhhh.hhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhhh...eeeeeeeee.........hhhhhhhhhhh........eeeee......eeeee.hhhhhhhhh....hhhhhhhhhhhh.....hhhhhh........hhhhh.eeeeee......hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wfm A   9 QQKHFVLVHGGCLGAWIWYKLKPLLESAGHKVTAVDLSAAGINPRRLDEIHTFRDYSEPLMEVMASIPPDEKVVLLGHSFGGMSLGLAMETYPEKISVAVFMSAMMPDPNHSLTYPFEKYNEKCPADMMLDSQFSTYGNPENPGMSMILGPQFMALKMFQNCSVEDLELAKMLTRPGSLFFQDLAKAKKFSTERYGSVKRAYIFCNEDKSFPVEFQKWFVESVGADKVKEIKEADAMGMLSQPREVCKCLLDISD 263
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258     


Chain B from PDB  Type:PROTEIN  Length:255
 aligned with PNAE_RAUSE | Q9SE93 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:255
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258     
           PNAE_RAUSE     9 QQKHFVLVHGGCLGAWIWYKLKPLLESAGHKVTAVDLSAAGINPRRLDEIHTFRDYSEPLMEVMASIPPDEKVVLLGHSFGGMSLGLAMETYPEKISVAVFMSAMMPDPNHSLTYPFEKYNEKCPADMMLDSQFSTYGNPENPGMSMILGPQFMALKMFQNCSVEDLELAKMLTRPGSLFFQDLAKAKKFSTERYGSVKRAYIFCNEDKSFPVEFQKWFVESVGADKVKEIKEADHMGMLSQPREVCKCLLDISD 263
               SCOP domains d2wfmb_ B: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2wfmB00 B:9-263  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh..eeeee..........hhhhh.hhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhhh...eeeeeeeee.........hhhhhhhhhhhhhhhhh..eeeee......eeeee.hhhhhhhhh....hhhhhhhhhhhh.....hhhhhhhh......hhhhh.eeeeee......hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wfm B   9 QQKHFVLVHGGCLGAWIWYKLKPLLESAGHKVTAVDLSAAGINPRRLDEIHTFRDYSEPLMEVMASIPPDEKVVLLGHSFGGMSLGLAMETYPEKISVAVFMSAMMPDPNHSLTYPFEKYNEKCPADMMLDSQFSTYGNPENPGMSMILGPQFMALKMFQNCSVEDLELAKMLTRPGSLFFQDLAKAKKFSTERYGSVKRAYIFCNEDKSFPVEFQKWFVESVGADKVKEIKEADAMGMLSQPREVCKCLLDISD 263
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258     


Chain C from PDB  Type:PROTEIN  Length:255
 aligned with PNAE_RAUSE | Q9SE93 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:255
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258     
           PNAE_RAUSE     9 QQKHFVLVHGGCLGAWIWYKLKPLLESAGHKVTAVDLSAAGINPRRLDEIHTFRDYSEPLMEVMASIPPDEKVVLLGHSFGGMSLGLAMETYPEKISVAVFMSAMMPDPNHSLTYPFEKYNEKCPADMMLDSQFSTYGNPENPGMSMILGPQFMALKMFQNCSVEDLELAKMLTRPGSLFFQDLAKAKKFSTERYGSVKRAYIFCNEDKSFPVEFQKWFVESVGADKVKEIKEADHMGMLSQPREVCKCLLDISD 263
               SCOP domains d2wfmc_ C: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2wfmC00 C:9-263  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh..eeeee..........hhhhh.hhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhhhhhhhh..eeeee......eeeee.hhhhhhhhh....hhhhhhhhhhhh.....hhhhhhhh......hhhhh.eeeeee......hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wfm C   9 QQKHFVLVHGGCLGAWIWYKLKPLLESAGHKVTAVDLSAAGINPRRLDEIHTFRDYSEPLMEVMASIPPDEKVVLLGHSFGGMSLGLAMETYPEKISVAVFMSAMMPDPNHSLTYPFEKYNEKCPADMMLDSQFSTYGNPENPGMSMILGPQFMALKMFQNCSVEDLELAKMLTRPGSLFFQDLAKAKKFSTERYGSVKRAYIFCNEDKSFPVEFQKWFVESVGADKVKEIKEADAMGMLSQPREVCKCLLDISD 263
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258     


Chain D from PDB  Type:PROTEIN  Length:255
 aligned with PNAE_RAUSE | Q9SE93 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:255
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258     
           PNAE_RAUSE     9 QQKHFVLVHGGCLGAWIWYKLKPLLESAGHKVTAVDLSAAGINPRRLDEIHTFRDYSEPLMEVMASIPPDEKVVLLGHSFGGMSLGLAMETYPEKISVAVFMSAMMPDPNHSLTYPFEKYNEKCPADMMLDSQFSTYGNPENPGMSMILGPQFMALKMFQNCSVEDLELAKMLTRPGSLFFQDLAKAKKFSTERYGSVKRAYIFCNEDKSFPVEFQKWFVESVGADKVKEIKEADHMGMLSQPREVCKCLLDISD 263
               SCOP domains d2wfmd_ D: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2wfmD00 D:9-263  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh..eeeee..........hhhhh.hhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhhh...eeeeeeeee.........hhhhhhhhhhh........eeeee......eeeee.hhhhhhhhh....hhhhhhhhhhhh.....hhhhhhhh......hhhhh.eeeeee......hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wfm D   9 QQKHFVLVHGGCLGAWIWYKLKPLLESAGHKVTAVDLSAAGINPRRLDEIHTFRDYSEPLMEVMASIPPDEKVVLLGHSFGGMSLGLAMETYPEKISVAVFMSAMMPDPNHSLTYPFEKYNEKCPADMMLDSQFSTYGNPENPGMSMILGPQFMALKMFQNCSVEDLELAKMLTRPGSLFFQDLAKAKKFSTERYGSVKRAYIFCNEDKSFPVEFQKWFVESVGADKVKEIKEADAMGMLSQPREVCKCLLDISD 263
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258     


Chain E from PDB  Type:PROTEIN  Length:255
 aligned with PNAE_RAUSE | Q9SE93 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:255
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258     
           PNAE_RAUSE     9 QQKHFVLVHGGCLGAWIWYKLKPLLESAGHKVTAVDLSAAGINPRRLDEIHTFRDYSEPLMEVMASIPPDEKVVLLGHSFGGMSLGLAMETYPEKISVAVFMSAMMPDPNHSLTYPFEKYNEKCPADMMLDSQFSTYGNPENPGMSMILGPQFMALKMFQNCSVEDLELAKMLTRPGSLFFQDLAKAKKFSTERYGSVKRAYIFCNEDKSFPVEFQKWFVESVGADKVKEIKEADHMGMLSQPREVCKCLLDISD 263
               SCOP domains d2wfme_ E: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2wfmE00 E:9-263  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                           CATH domains
           Pfam domains (1) ----Abhydrolase_6-2wfmE01 E:13-256                                                                                                                                                                                                                      ------- Pfam domains (1)
           Pfam domains (2) ----Abhydrolase_6-2wfmE02 E:13-256                                                                                                                                                                                                                      ------- Pfam domains (2)
           Pfam domains (3) ----Abhydrolase_6-2wfmE03 E:13-256                                                                                                                                                                                                                      ------- Pfam domains (3)
           Pfam domains (4) ----Abhydrolase_6-2wfmE04 E:13-256                                                                                                                                                                                                                      ------- Pfam domains (4)
           Pfam domains (5) ----Abhydrolase_6-2wfmE05 E:13-256                                                                                                                                                                                                                      ------- Pfam domains (5)
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh..eeeee..........hhhhh.hhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhh........eeeeee....eeeeee.hhhhhhhhh....hhhhhhhhhhhh.....hhhhhh........hhhhheeeeeee......hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wfm E   9 QQKHFVLVHGGCLGAWIWYKLKPLLESAGHKVTAVDLSAAGINPRRLDEIHTFRDYSEPLMEVMASIPPDEKVVLLGHSFGGMSLGLAMETYPEKISVAVFMSAMMPDPNHSLTYPFEKYNEKCPADMMLDSQFSTYGNPENPGMSMILGPQFMALKMFQNCSVEDLELAKMLTRPGSLFFQDLAKAKKFSTERYGSVKRAYIFCNEDKSFPVEFQKWFVESVGADKVKEIKEADAMGMLSQPREVCKCLLDISD 263
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258
   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, 5)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 5)

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

(-) Pfam Domains  (1, 5)

Asymmetric Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (PNAE_RAUSE | Q9SE93)
molecular function
    GO:0052689    carboxylic ester hydrolase activity    Catalysis of the hydrolysis of a carboxylic ester bond.
    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:0050529    polyneuridine-aldehyde esterase activity    Catalysis of the reaction: H(2)O + polyneuridine aldehyde = 16-epivellosimine + CO(2) + methanol.
biological process
    GO:0009820    alkaloid metabolic process    The chemical reactions and pathways involving alkaloids, nitrogen containing natural products which are not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases).

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 Related Entries

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

UniProtKB/Swiss-Prot
        PNAE_RAUSE | Q9SE93: 2wfl 3gzj

(-) Related Entries Specified in the PDB File

2wfl CRYSTAL STRUCTURE OF POLYNEURIDINE ALDEHYDE ESTERASE