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(-) Description

Title :  CRYSTAL STRUCTURE OF SALICYLATE 1,2-DIOXYGENASE FROM PSEUDOAMINOBACTER SALICYLATOXIDANS ADDUCTS WITH NAPHTHOATE
 
Authors :  M. Ferraroni, F. Briganti, I. Matera
Date :  21 Jun 10  (Deposition) - 13 Jul 11  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Beta-Sandwich, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Ferraroni, I. Matera, L. Steimer, S. Burger, A. Scozzafava, A. Stolz, F. Briganti
Crystal Structures Of Salicylate 1, 2-Dioxygenase-Substrates Adducts: A Step Towards The Comprehension Of The Structural Basis For Substrate Selection In Class Iii Ring Cleaving Dioxygenases.
J. Struct. Biol. V. 177 431 2012
PubMed-ID: 22155290  |  Reference-DOI: 10.1016/J.JSB.2011.11.026

(-) Compounds

Molecule 1 - GENTISATE 1,2-DIOXYGENASE
    Chains: A
    EC Number: 1.13.11.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDAMINOBACTER SALICYLATOXIDANS
    Organism Taxid: 93369
    Strain: BN12

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
11HN1Ligand/Ion1-HYDROXYNAPHTHALENE-2-CARBOXYLIC ACID
2FE21Ligand/IonFE (II) ION
3GOL2Ligand/IonGLYCEROL
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
11HN4Ligand/Ion1-HYDROXYNAPHTHALENE-2-CARBOXYLIC ACID
2FE24Ligand/IonFE (II) ION
3GOL8Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:119 , HIS A:121 , HIS A:160 , 1HN A:370BINDING SITE FOR RESIDUE FE2 A 369
2AC2SOFTWAREMET A:46 , ARG A:83 , TRP A:104 , GLN A:108 , HIS A:119 , HIS A:121 , ARG A:127 , HIS A:160 , HIS A:162 , ASP A:174 , LEU A:176 , ILE A:178 , FE2 A:369BINDING SITE FOR RESIDUE 1HN A 370
3AC3SOFTWARELEU A:219 , ARG A:265 , GLU A:282 , ARG A:295 , GLU A:297 , ARG A:347 , HOH A:416 , HOH A:462 , HOH A:594BINDING SITE FOR RESIDUE GOL A 371
4AC4SOFTWAREPHE A:204 , GLU A:208 , CYS A:212 , HIS A:213 , PHE A:237 , HOH A:679BINDING SITE FOR RESIDUE GOL A 372

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NKT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NKT)

(-) 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:364
 aligned with Q67FT0_PSESE | Q67FT0 from UniProtKB/TrEMBL  Length:368

    Alignment length:364
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363    
         Q67FT0_PSESE     4 EKLDHESVTQAMQPKDTPELRALYKSFEEESIIPLWTQLGDLMPIHPKSKAVPHVWKWSTLLRLARKSGELVPVGRGGERRALGLANPGLGGNAYISPTMWAGIQYLGPRETAPEHRHSQNAFRFVVEGEGVWTVVNGDPVRMSRGDLLLTPGWCFHGHHNDTDQPMAWIDGLDIPFSQQMDVGFFEFGSDRVTDYATPNFSRGERLWCHPGLRPLSGLQNTVASPIGAYRWEFTDRALTEQLLLEDEGQPATVAPGHAAIRYVNPTTGGDVMPTLRCEFHRLRAGTETATRNEVGSTVFQVFEGAGAVVMNGETTKLEKGDMFVVPSWVPWSLQAETQFDLFRFSDAPIMEALSFMRTKIEGQ 367
               SCOP domains d3nkta_ A: automated matches                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhh...hhhhhhhhhh..........eeehhhhhhhhhhhhhhhh.........eee................eeeeeee....eeeeeee...eeee....eeeeeee..eeeeee...eeee.....eeeee.....eeeeeeehhhhhhhhh...eee.............hhhhhhhh...................eehhhhhhhhhhhhhhhhhh.........eeeee..............eeeeeee........eee...eeeeeee..eeeee..eeeee....eeee.....eeeee...eeeeeeehhhhhhhh....eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nkt A   4 EKLDHESVTQAMQPKDTPELRALYKSFEEESIIPLWTQLGDLMPIHPKSKAVPHVWKWSTLLRLARKSGELVPVGRGGERRALGLANPGLGGNAYISPTMWAGIQYLGPRETAPEHRHSQNAFRFVVEGEGVWTVVNGDPVRMSRGDLLLTPGWCFHGHMNDTDQPMAWIDGLDIPFSQQMDVGFFEFGSDRVTDYATPNFSRGERLWCHPGLRPLSGLQNTVASPIGAYRWEFTDRALTEQLLLEDEGQPATVAPGHAAIRYVNPTTGGDVMPTLRCEFHRLRAGTETATRNEVGSTVFQVFEGAGAVVMNGETTKLEKGDMFVVPSWVPWSLQAETQFDLFRFSDAPIMEALSFMRTKIEGQ 367
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q67FT0_PSESE | Q67FT0)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q67FT0_PSESE | Q67FT0: 2phd 3njz 3nl1 3nst 3nvc 3nw4 4fag 4fah 4fbf

(-) Related Entries Specified in the PDB File

2phd CRYSTAL STRUCTURE OF NATIVE SALICYLATE 1,2-DIOXYGENASE FROM PSEUDOAMINOBACTER SALICYLATOXIDANS
3njz CRYSTAL STRUCTURE OF SALICYLATE 1,2-DIOXYGENASE FROM PSEUDOAMINOBACTER SALICYLATOXIDANS ADDUCTS WITH SALICYLATE
3nl1 CRYSTAL STRUCTURE OF SALICYLATE 1,2-DIOXYGENASE FROM PSEUDOAMINOBACTER SALICYLATOXIDANS ADDUCTS WITH GENTISATE
3nst CRYSTAL STRUCTURE OF SALICYLATE 1,2-DIOXYGENASE G106A MUTANT FROM PSEUDOAMINOBACTER SALICYLATOXIDANS