Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF POLYNEURIDINE ALDEHYDE ESTERASE
 
Authors :  L. Yang, M. Hill, S. Panjikar, M. Wang, J. Stoeckigt
Date :  08 Apr 09  (Deposition) - 18 Aug 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (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
    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
    Organism Common: SERPENTWOOD
    Organism Scientific: RAUVOLFIA SERPENTINA
    Organism Taxid: 4060
 
Molecule 2 - POLYNEURIDINE-ALDEHYDE ESTERASE
    Chains: B
    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
    Organism Common: SERPENTWOOD
    Organism Scientific: RAUVOLFIA SERPENTINA
    Organism Taxid: 4060

 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  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CME3Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CME1Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:152 , MET B:153 , SER B:186 , PHE B:188 , PHE B:189 , GLN B:190 , HOH B:2099 , HOH B:2151 , HOH B:2152 , HOH B:2153BINDING SITE FOR RESIDUE SO4 B1264
2AC2SOFTWARESER A:87 , SER A:218 , HIS A:244 , HOH A:2001 , HOH A:2150BINDING SITE FOR RESIDUE SO4 A1264

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WFL)

(-) 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 d2wfla_ A: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2wflA00 A:9-263  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh..eeeee..........hhhhh.hhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhh........eeeee......eeeee.hhhhhhhhh....hhhhhhhhhhhh..ee.hhhhhh........hhhhh.eeeeee......hhhhhhhhhhhhh..eeeee.....hhhhhh.....hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wfl A   9 QQKHFVLVHGGCLGAWIWYKLKPLLESAGHKVTAVDLSAAGINPRRLDEIHTFRDYSEPLMEVMASIPPDEKVVLLGHSFGGMSLGLAMETYPEKISVAVFMSAMMPDPNHSLTYPFEKYNEKCPADMMLDSQFSTYGNPENPGMSMILGPQFMALKMFQNCSVEDLELAKMLTRPGSLFFQDLAKAKKFSTERYGSVKRAYIFCNEDKSFPVEFQKWFVESVGADKVKEIKEADHMGMLSQPREVcKCLLDISD 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     
                                                                                                                                                                                                                                                                                255-CME    


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 d2wflb_ B: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2wflB00 B:9-263  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                           CATH domains
           Pfam domains (1) ----Abhydrolase_6-2wflB01 B:13-256                                                                                                                                                                                                                      ------- Pfam domains (1)
           Pfam domains (2) ----Abhydrolase_6-2wflB02 B:13-256                                                                                                                                                                                                                      ------- Pfam domains (2)
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh..eeeee..........hhhhh.hhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhh........eeeee......eeeee.hhhhhhhhh....hhhhhhhhhhhh.....hhhhhh........hhhhh.eeeeee......hhhhhhhhhhhhh..eeeee.....hhhhhh.......hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wfl B   9 QQKHFVLVHGGCLGAWIWYKLKPLLESAGHKVTAVDLSAAGINPRRLDEIHTFRDYSEPLMEVMASIPPDEKVVLLGHSFGGMSLGLAMETYPEKISVAVFMSAMMPDPNHSLTYPFEKYNEKCPADMMLDSQFSTYGNPENPGMSMILGPQFMALKMFQNCSVEDLELAKMLTRPGSLFFQDLAKAKKFSTERYGSVKRAYIFCNEDKSFPVEFQKWFVESVGADKVKEIKEADHMGMLSQPREVcKcLLDISD 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     
                                                                                                                                                                                                                                                                                255-CME    
                                                                                                                                                                                                                                                                                  257-CME
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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).

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2wfl)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2wfl
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PNAE_RAUSE | Q9SE93
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.1.78
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PNAE_RAUSE | Q9SE93
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2wfm CRYSTAL STRUCTURE OF POLYNEURIDINE ALDEHYDE ESTERASE