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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE FE(II)/ALPHA-KETOGLUTARATE DEPENDENT TAURINE DIOXYGENASE FROM PSEUDOMONAS PUTIDA KT2440
 
Authors :  S. H. Knauer, H. Dobbek
Date :  09 Dec 11  (Deposition) - 18 Jan 12  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.57
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Jelly Roll Motif, Dioxygenase, Fe(Ii), Alpha-Ketoglutarate, Taurine, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. H. Knauer, O. Hartl-Spiegelhauer, S. Schwarzinger, P. Hanzelmann H. Dobbek
The Fe(Ii) / Alpha-Ketoglutarate Dependent Taurine Dioxygenases From Pseudomonas Putida And Escherichia Coli Are Tetramers
Febs J. V. 279 816 2012
PubMed-ID: 22221834  |  Reference-DOI: 10.1111/J.1742-4658.2012.08473.X

(-) Compounds

Molecule 1 - ALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE
    Chains: A, C, B, D
    EC Number: 1.14.11.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PP0230, PP_0230, TAUD
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 160488
    Strain: KT2440

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1AKG4Ligand/Ion2-OXOGLUTARIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:112 , THR A:124 , HIS A:253 , ARG A:264 , ARG A:268BINDING SITE FOR RESIDUE AKG A 279
2AC2SOFTWAREASP C:99 , LEU C:112 , THR C:124 , TRP C:246 , HIS C:253 , ARG C:264 , ARG C:268BINDING SITE FOR RESIDUE AKG C 279
3AC3SOFTWAREASN B:93 , THR B:124 , HIS B:253 , ALA B:255 , ARG B:264BINDING SITE FOR RESIDUE AKG B 279
4AC4SOFTWARELEU D:83 , ASN D:93 , HIS D:97 , THR D:124 , TRP D:246 , HIS D:253 , ARG D:264 , MET D:266 , ARG D:268 , HOH D:335BINDING SITE FOR RESIDUE AKG D 279

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V17)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Arg A:260 -Pro A:261
2Arg C:260 -Pro C:261
3Pro B:72 -Asn B:73
4Asn B:73 -Val B:74
5Arg B:260 -Pro B:261
6Arg D:260 -Pro D:261

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V17)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V17)

(-) Exons   (0, 0)

(no "Exon" information available for 3V17)

(-) 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:276
 aligned with Q88RA3_PSEPK | Q88RA3 from UniProtKB/TrEMBL  Length:277

    Alignment length:276
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271      
         Q88RA3_PSEPK     2 SLTITPLSPALGAQISGVDISRDISAEERDAIEQALLQHQVLFLRDQPINPEQQARFAARFGDLHIHPIYPNVPDTPQVLVLDTAVTDVRDNAVWHTDVTFLPTPALGAVLSAKQLPAYGGDTLWASGIAAFEALSAPLREMLDGLTATHDFTKSFPLERFGTTPQDLARWEATRRNNPPLSHPVVRTHPVSGRKALFVNEGFTTRINELSELESDALLRLLFAHATRPEFSIRWRWQENDVAFWDNRVTQHFAVDDYRPNRRVMHRATILGDAPF 277
               SCOP domains d3v17a_ A: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee......eeee........hhhhhhhhhhhhhhhheeee.....hhhhhhhhhhhhh.........ee..eeeeeeee.....hhhhh..............eeeeeeee.......eeeeehhhhhhhhhhhhhhhhh..eeee.hhhh.hhhhhh.hhhhhhhhhhhhhhh..eeee.eee......eee......eeee...hhhhhhhhhhhhhhhhhhhh.eeee......eeeee...eeeee.........eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v17 A   2 SLTITPLSPALGAQISGVDISRDISAEERDAIEQALLQHQVLFLRDQPINPEQQARFAARFGDLHIHPIYPNVPDTPQVLVLDTAVTDVRDNAVWHTDVTFLPTPALGAVLSAKQLPAYGGDTLWASGIAAFEALSAPLREMLDGLTATHDFTKSFPLERFGTTPQDLARWEATRRNNPPLSHPVVRTHPVSGRKALFVNEGFTTRINELSELESDALLRLLFAHATRPEFSIRWRWQENDVAFWDNRVTQHFAVDDYRPNRRVMHRATILGDAPF 277
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271      


Chain B from PDB  Type:PROTEIN  Length:276
 aligned with Q88RA3_PSEPK | Q88RA3 from UniProtKB/TrEMBL  Length:277

    Alignment length:276
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271      
         Q88RA3_PSEPK     2 SLTITPLSPALGAQISGVDISRDISAEERDAIEQALLQHQVLFLRDQPINPEQQARFAARFGDLHIHPIYPNVPDTPQVLVLDTAVTDVRDNAVWHTDVTFLPTPALGAVLSAKQLPAYGGDTLWASGIAAFEALSAPLREMLDGLTATHDFTKSFPLERFGTTPQDLARWEATRRNNPPLSHPVVRTHPVSGRKALFVNEGFTTRINELSELESDALLRLLFAHATRPEFSIRWRWQENDVAFWDNRVTQHFAVDDYRPNRRVMHRATILGDAPF 277
               SCOP domains d3v17b_ B: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee......eeee........hhhhhhhhhhhhhhhheeee.....hhhhhhhhhhhhh................eeeee.....hhhhh..............eeeeeeee.......eeeeehhhhhhhhhhhhhhhhh..eeee.hhhh.hhhhh..hhhhhhhhhhhhhhh..eeee.eee......eee......eeee...hhhhhhhhhhhhhhhhhhhh.eeee......eeeee...eeeee.........eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v17 B   2 SLTITPLSPALGAQISGVDISRDISAEERDAIEQALLQHQVLFLRDQPINPEQQARFAARFGDLHIHPIYPNVPDTPQVLVLDTAVTDVRDNAVWHTDVTFLPTPALGAVLSAKQLPAYGGDTLWASGIAAFEALSAPLREMLDGLTATHDFTKSFPLERFGTTPQDLARWEATRRNNPPLSHPVVRTHPVSGRKALFVNEGFTTRINELSELESDALLRLLFAHATRPEFSIRWRWQENDVAFWDNRVTQHFAVDDYRPNRRVMHRATILGDAPF 277
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271      


Chain C from PDB  Type:PROTEIN  Length:276
 aligned with Q88RA3_PSEPK | Q88RA3 from UniProtKB/TrEMBL  Length:277

    Alignment length:276
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271      
         Q88RA3_PSEPK     2 SLTITPLSPALGAQISGVDISRDISAEERDAIEQALLQHQVLFLRDQPINPEQQARFAARFGDLHIHPIYPNVPDTPQVLVLDTAVTDVRDNAVWHTDVTFLPTPALGAVLSAKQLPAYGGDTLWASGIAAFEALSAPLREMLDGLTATHDFTKSFPLERFGTTPQDLARWEATRRNNPPLSHPVVRTHPVSGRKALFVNEGFTTRINELSELESDALLRLLFAHATRPEFSIRWRWQENDVAFWDNRVTQHFAVDDYRPNRRVMHRATILGDAPF 277
               SCOP domains d3v17c_ C: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee......eeee........hhhhhhhhhhhhhhhheeee.....hhhhhhhhhhhhh.........ee..eeeeeeee.....hhhhh..............eeeeeeee.......eeeeehhhhhhhhhhhhhhhhh..eeee.hhhh........hhhhhhhhhhhhhhh..eeee.eee......eee......eeee...hhhhhhhhhhhhhhhhhhhh.eeee......eeeee...eeeee.........eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v17 C   2 SLTITPLSPALGAQISGVDISRDISAEERDAIEQALLQHQVLFLRDQPINPEQQARFAARFGDLHIHPIYPNVPDTPQVLVLDTAVTDVRDNAVWHTDVTFLPTPALGAVLSAKQLPAYGGDTLWASGIAAFEALSAPLREMLDGLTATHDFTKSFPLERFGTTPQDLARWEATRRNNPPLSHPVVRTHPVSGRKALFVNEGFTTRINELSELESDALLRLLFAHATRPEFSIRWRWQENDVAFWDNRVTQHFAVDDYRPNRRVMHRATILGDAPF 277
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271      


Chain D from PDB  Type:PROTEIN  Length:276
 aligned with Q88RA3_PSEPK | Q88RA3 from UniProtKB/TrEMBL  Length:277

    Alignment length:276
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271      
         Q88RA3_PSEPK     2 SLTITPLSPALGAQISGVDISRDISAEERDAIEQALLQHQVLFLRDQPINPEQQARFAARFGDLHIHPIYPNVPDTPQVLVLDTAVTDVRDNAVWHTDVTFLPTPALGAVLSAKQLPAYGGDTLWASGIAAFEALSAPLREMLDGLTATHDFTKSFPLERFGTTPQDLARWEATRRNNPPLSHPVVRTHPVSGRKALFVNEGFTTRINELSELESDALLRLLFAHATRPEFSIRWRWQENDVAFWDNRVTQHFAVDDYRPNRRVMHRATILGDAPF 277
               SCOP domains d3v17d_ D: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee......eeee........hhhhhhhhhhhhhhhheeee.....hhhhhhhhhhhhh................eeeee.....hhhhh..............eeeeeeee.......eeeeehhhhhhhhhhhhhhhhh..eeee.hhhh...........hhhhhhhhhhhh..eeee.eee......eee......eeee...hhhhhhhhhhhhhhhhhhhh.eeee......eeeee...eeeee.........eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v17 D   2 SLTITPLSPALGAQISGVDISRDISAEERDAIEQALLQHQVLFLRDQPINPEQQARFAARFGDLHIHPIYPNVPDTPQVLVLDTAVTDVRDNAVWHTDVTFLPTPALGAVLSAKQLPAYGGDTLWASGIAAFEALSAPLREMLDGLTATHDFTKSFPLERFGTTPQDLARWEATRRNNPPLSHPVVRTHPVSGRKALFVNEGFTTRINELSELESDALLRLLFAHATRPEFSIRWRWQENDVAFWDNRVTQHFAVDDYRPNRRVMHRATILGDAPF 277
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
   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, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V17)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V17)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q88RA3_PSEPK | Q88RA3)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    AKG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:260 - Pro A:261   [ RasMol ]  
    Arg B:260 - Pro B:261   [ RasMol ]  
    Arg C:260 - Pro C:261   [ RasMol ]  
    Arg D:260 - Pro D:261   [ RasMol ]  
    Asn B:73 - Val B:74   [ RasMol ]  
    Pro B:72 - Asn B:73   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  3v17
    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
  Q88RA3_PSEPK | Q88RA3
    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)
  1.14.11.17
    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
  Q88RA3_PSEPK | Q88RA3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q88RA3_PSEPK | Q88RA3: 3pvj 3v15

(-) Related Entries Specified in the PDB File

3pvj CRYSTAL STRUCTURE OF THE FE(II)/ALPHA-KETOGLUTARATE DEPENDENT TAURINE DIOXYGENASE FROM PSEUDOMONAS PUTIDA KT2440
3v15 CRYSTAL STRUCTURE OF THE FE(II)/ALPHA-KETOGLUTARATE DEPENDENT TAURINE DIOXYGENASE FROM PSEUDOMONAS PUTIDA KT2440