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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  ENTEROBACTER SP. PX6-4 FERULIC ACID DECARBOXYLASE IN COMPLEX WITH SUBSTRATE ANALOGUES
 
Authors :  W. Gu, J. K. Yang, Z. Y. Lou, Z. H. Meng, K. -Q. Zhang
Date :  12 Jul 10  (Deposition) - 16 Feb 11  (Release) - 16 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Ferulic Acid, Decarboxylase, 4-Vinylguaiacol, Catalytic Mechanism, Phenolic Acid Decarboxylase Superfamily, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Gu, J. K. Yang, Z. Y. Lou, L. M. Liang, Y. Sun, J. W. Huang, X. M. Li, Y. Cao, Z. H. Meng, K. -Q. Zhang
Structural Basis Of Enzymatic Activity For The Ferulic Acid Decarboxylase (Fadase) From Enterobacter Sp. Px6-4
Plos One V. 6 E1626 2011
PubMed-ID: 21283705  |  Reference-DOI: 10.1371/JOURNAL.PONE.0016262

(-) Compounds

Molecule 1 - FERULIC ACID DECARBOXYLASE
    Chains: A, B
    EC Number: 4.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ENTEROBACTER SP. PX6-4
    Organism Taxid: 418698

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1FER1Ligand/Ion3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FER1Ligand/Ion3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1FER-1Ligand/Ion3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1FER1Ligand/Ion3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:21 , ASN A:23 , TYR A:27 , VAL A:46 , PHE A:95 , GLU A:134 , HOH A:284BINDING SITE FOR RESIDUE FER A 169

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NX2)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:127 -Pro A:128
2Phe A:163 -Pro A:164
3Tyr B:127 -Pro B:128
4Phe B:163 -Pro B:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NX2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NX2)

(-) Exons   (0, 0)

(no "Exon" information available for 3NX2)

(-) 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:162
 aligned with C6F3U5_9ENTR | C6F3U5 from UniProtKB/TrEMBL  Length:168

    Alignment length:162
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  
         C6F3U5_9ENTR     5 DKHDLSGFVGKHLVYTYDNGWEYEIYVKNENTLDYRIHSGLVGNRWVKDQQAYIVRVGESIYKISWTEPTGTDVSLIVNLGDSLFHGTIFFPRWVMNNPEKTVCFQNDHIPLMNSYRDAGPAYPTEVIDEFATITFVRDCGANNESVIACAASELPKNFPDN 166
               SCOP domains d3nx2a_ A: automated matches                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeee.....eeeeeeee..eeeeee........eeeeee.eeeeee..eeeeeee.....eeeeeee....eeeeeeeehhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....eeeeeeeeeeeeee...........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nx2 A   5 DKHDLSGFVGKHLVYTYDNGWNYEIYVKNDNTIDYRIHSGLVGNRWVKDQEAYIVRVGESIYKISWTEPTGTDVSLIVNLGDSLFHGTIFFPRWVMNNPEPTVCFQNDHIPLMNSYREAGPAYPTEVIDEFATITFVRDCGANNESVIACAASELPKNFPDN 166
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  


Chain B from PDB  Type:PROTEIN  Length:164
 aligned with C6F3U5_9ENTR | C6F3U5 from UniProtKB/TrEMBL  Length:168

    Alignment length:164
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162    
         C6F3U5_9ENTR     3 TFDKHDLSGFVGKHLVYTYDNGWEYEIYVKNENTLDYRIHSGLVGNRWVKDQQAYIVRVGESIYKISWTEPTGTDVSLIVNLGDSLFHGTIFFPRWVMNNPEKTVCFQNDHIPLMNSYRDAGPAYPTEVIDEFATITFVRDCGANNESVIACAASELPKNFPDN 166
               SCOP domains d3nx2b_ B: automated matches                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------PA_decarbox-3nx2B01 B:9-166                                                                                                                                    Pfam domains (1)
           Pfam domains (2) ------PA_decarbox-3nx2B02 B:9-166                                                                                                                                    Pfam domains (2)
         Sec.struct. author ............eeeeeee....eeeeeeee..eeeeee........eeeeee.eeeeee..eeeeeee.....eeeeeee....eeeeeeeehhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....eeeeeeeeeeeeee...........hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nx2 B   3 TFDKHDLSGFVGKHLVYTYDNGWNYEIYVKNDNTIDYRIHSGLVGNRWVKDQEAYIVRVGESIYKISWTEPTGTDVSLIVNLGDSLFHGTIFFPRWVMNNPEPTVCFQNDHIPLMNSYREAGPAYPTEVIDEFATITFVRDCGANNESVIACAASELPKNFPDN 166
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162
   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: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NX2)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: PA_decarbox] (4)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (C6F3U5_9ENTR | C6F3U5)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.

 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
    FER  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:163 - Pro A:164   [ RasMol ]  
    Phe B:163 - Pro B:164   [ RasMol ]  
    Tyr A:127 - Pro A:128   [ RasMol ]  
    Tyr B:127 - Pro B:128   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  3nx2
    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
  C6F3U5_9ENTR | C6F3U5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  4.1.1.-
    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
  C6F3U5_9ENTR | C6F3U5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        C6F3U5_9ENTR | C6F3U5: 3nx1 4uu2 4uu3

(-) Related Entries Specified in the PDB File

3nx1 SAME PROTEIN, APO FORM