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(-) Description

Title :  CRYSTAL STRUCTURE DETERMINATION OF A SALICYLATE 1,2-DIOXYGENASE FROM PSEUDAMINOBACTER SALICYLATOXIDANS
 
Authors :  I. Matera, M. Ferraroni, F. Briganti
Date :  11 Apr 07  (Deposition) - 22 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta-Sandwich, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Ferraroni, I. Matera, F. Briganti, A. Stolz, S. Burger
Crystal Structure Determination Of A Salicylate 1, 2-Dioxygenase From Pseudaminobacter Salicylatoxidans
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GENTISATE 1,2-DIOXYGENASE
    Chains: A, B, C, D
    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

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL4Ligand/IonCHLORIDE ION
3FE4Ligand/IonFE (III) ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:119 , HIS A:121 , HIS A:160 , ACT A:371BINDING SITE FOR RESIDUE FE A 370
02AC2SOFTWAREHIS B:119 , HIS B:121 , HIS B:160 , HOH B:419 , ACT D:1BINDING SITE FOR RESIDUE FE B 370
03AC3SOFTWAREHIS C:119 , HIS C:121 , HIS C:160 , HOH C:382 , HOH C:432BINDING SITE FOR RESIDUE FE C 370
04AC4SOFTWAREHIS D:119 , HIS D:121 , HIS D:160 , HOH D:374BINDING SITE FOR RESIDUE FE D 370
05AC5SOFTWAREARG A:265 , GLU A:282 , ARG A:347 , HOH A:376 , HOH A:390BINDING SITE FOR RESIDUE CL A 1
06AC6SOFTWAREGLU B:282 , HOH B:379 , HOH B:408BINDING SITE FOR RESIDUE CL B 2
07AC7SOFTWAREGLU D:282 , ARG D:347 , HOH D:393BINDING SITE FOR RESIDUE CL D 3
08AC8SOFTWAREARG C:295 , GLU C:297 , ARG C:347 , HOH C:414BINDING SITE FOR RESIDUE CL C 4
09AC9SOFTWAREASP A:174 , LEU A:176 , FE A:370 , LEU C:38BINDING SITE FOR RESIDUE ACT A 371
10BC1SOFTWAREHIS B:119 , HIS B:121 , FE B:370 , HOH B:419 , LEU D:38 , MET D:46BINDING SITE FOR RESIDUE ACT D 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:193 -Asp A:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PHD)

(-) 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:349
 aligned with Q67FT0_PSESE | Q67FT0 from UniProtKB/TrEMBL  Length:368

    Alignment length:351
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366 
         Q67FT0_PSESE    17 PKDTPELRALYKSFEEESIIPLWTQLGDLMPIHPKSKAVPHVWKWSTLLRLARKSGELVPVGRGGERRALGLANPGLGGNAYISPTMWAGIQYLGPRETAPEHRHSQNAFRFVVEGEGVWTVVNGDPVRMSRGDLLLTPGWCFHGHHNDTDQPMAWIDGLDIPFSQQMDVGFFEFGSDRVTDYATPNFSRGERLWCHPGLRPLSGLQNTVASPIGAYRWEFTDRALTEQLLLEDEGQPATVAPGHAAIRYVNPTTGGDVMPTLRCEFHRLRAGTETATRNEVGSTVFQVFEGAGAVVMNGETTKLEKGDMFVVPSWVPWSLQAETQFDLFRFSDAPIMEALSFMRTKIEGQ 367
               SCOP domains d2phda1 A:17-367 Gentisate 1,2-dioxygenase                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhheee....hhhhh..........eeehhhhhhhhhhhh.............eeee...............eeeeeee....eeeeeee...eeeeeee.eeeeeee..eeeeee...eeee.....eeeee.....eeeeeeehhhhhhhh....eee...--........hhhhhhhh...eee.hhh.........eehhhhhhhhhhhhhhhhhh.........eeeeee.............eeeeeee........eee...eeeeeee..eeeee..eeeee....eeee.....eeeee...eeeeeeehhhhhhhh....eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2phd A  17 PKDTPELRALYKSFEEESIIPLWTQLGDLMPIHPKSKAVPHVWKWSTLLRLARKSGELVPVGRGGERRALGLANPGLGGNAYISPTMWAGIQYLGPRETAPEHRHSQNAFRFVVEGEGVWTVVNGDPVRMSRGDLLLTPGWCFHGHMNDTDQPMAWIDGLDIPFSQQMDVGFFEFGSD--TDYATPNFSRGERLWCHPGLRPLSGLQNTVASPIGAYRWEFTDRALTEQLLLEDEGQPATVAPGHAAIRYVNPTTGGDVMPTLRCEFHRLRAGTETATRNEVGSTVFQVFEGAGAVVMNGETTKLEKGDMFVVPSWVPWSLQAETQFDLFRFSDAPIMEALSFMRTKIEGQ 367
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       | -|      206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366 
                                                                                                                                                                                                           194  |                                                                                                                                                                          
                                                                                                                                                                                                              197                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:348
 aligned with Q67FT0_PSESE | Q67FT0 from UniProtKB/TrEMBL  Length:368

    Alignment length:353
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365   
         Q67FT0_PSESE    16 QPKDTPELRALYKSFEEESIIPLWTQLGDLMPIHPKSKAVPHVWKWSTLLRLARKSGELVPVGRGGERRALGLANPGLGGNAYISPTMWAGIQYLGPRETAPEHRHSQNAFRFVVEGEGVWTVVNGDPVRMSRGDLLLTPGWCFHGHHNDTDQPMAWIDGLDIPFSQQMDVGFFEFGSDRVTDYATPNFSRGERLWCHPGLRPLSGLQNTVASPIGAYRWEFTDRALTEQLLLEDEGQPATVAPGHAAIRYVNPTTGGDVMPTLRCEFHRLRAGTETATRNEVGSTVFQVFEGAGAVVMNGETTKLEKGDMFVVPSWVPWSLQAETQFDLFRFSDAPIMEALSFMRTKIEGQK 368
               SCOP domains d2phdb_ B: automated matches                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.eee...................eeehhhhhhhhhhhhhhhhhhhh--...eeee...............eeeeeee....eeeeeee...eeeeeee.eeeeeee..eeeeee...eeee.....eeeee.....eeeeeeehhhhhhhhh...eee...---.......hhhhhhhh...eee.hhh.........eehhhhhhhhhhhhhhhhhh.........eeeeee.............eeeeeee........eee...eeeeeee..eeeee..eeeee....eeee.....eeeee...eeeeeeehhhhhhhh....eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2phd B  16 QPKDTPELRALYKSFEEESIIPLWTQLGDLMPIHPKSKAVPHVWKWSTLLRLARKSGELVPVGR--ERRALGLANPGLGGNAYISPTMWAGIQYLGPRETAPEHRHSQNAFRFVVEGEGVWTVVNGDPVRMSRGDLLLTPGWCFHGHMNDTDQPMAWIDGLDIPFSQQMDVGFFEFGSD---DYATPNFSRGERLWCHPGLRPLSGLQNTVASPIGAYRWEFTDRALTEQLLLEDEGQPATVAPGHAAIRYVNPTTGGDVMPTLRCEFHRLRAGTETATRNEVGSTVFQVFEGAGAVVMNGETTKLEKGDMFVVPSWVPWSLQAETQFDLFRFSDAPIMEALSFMRTKIEGQK 368
                                    25        35        45        55        65        75   |  | 85        95       105       115       125       135       145       155       165       175       185        |-  |    205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365   
                                                                                          79 82                                                                                                             194 198                                                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:348
 aligned with Q67FT0_PSESE | Q67FT0 from UniProtKB/TrEMBL  Length:368

    Alignment length:352
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365  
         Q67FT0_PSESE    16 QPKDTPELRALYKSFEEESIIPLWTQLGDLMPIHPKSKAVPHVWKWSTLLRLARKSGELVPVGRGGERRALGLANPGLGGNAYISPTMWAGIQYLGPRETAPEHRHSQNAFRFVVEGEGVWTVVNGDPVRMSRGDLLLTPGWCFHGHHNDTDQPMAWIDGLDIPFSQQMDVGFFEFGSDRVTDYATPNFSRGERLWCHPGLRPLSGLQNTVASPIGAYRWEFTDRALTEQLLLEDEGQPATVAPGHAAIRYVNPTTGGDVMPTLRCEFHRLRAGTETATRNEVGSTVFQVFEGAGAVVMNGETTKLEKGDMFVVPSWVPWSLQAETQFDLFRFSDAPIMEALSFMRTKIEGQ 367
               SCOP domains d2phdc_ C: automated matches                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh.eee....hhhhh..........eeehhhhhhhhhhhhhh....--.....eeee...............eeeeeee....eeeeeee...eeeeeee.eeeeeee..eeeeee...eeee.....eeeee.....eeeeeeehhhhhhhh....eee....--.......hhhhhhhh...eee.hhh.........eehhhhhhhhhhhhhhhhhh.........eeeeee.............eeeeeee........eee...eeeeeee..eeeee..eeeee....eeee.....eeeee...eeeeeeehhhhhhhh....eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2phd C  16 QPKDTPELRALYKSFEEESIIPLWTQLGDLMPIHPKSKAVPHVWKWSTLLRLARKSGELVPV--GGERRALGLANPGLGGNAYISPTMWAGIQYLGPRETAPEHRHSQNAFRFVVEGEGVWTVVNGDPVRMSRGDLLLTPGWCFHGHMNDTDQPMAWIDGLDIPFSQQMDVGFFEFGSDR--DYATPNFSRGERLWCHPGLRPLSGLQNTVASPIGAYRWEFTDRALTEQLLLEDEGQPATVAPGHAAIRYVNPTTGGDVMPTLRCEFHRLRAGTETATRNEVGSTVFQVFEGAGAVVMNGETTKLEKGDMFVVPSWVPWSLQAETQFDLFRFSDAPIMEALSFMRTKIEGQ 367
                                    25        35        45        55        65        75 |  |   85        95       105       115       125       135       145       155       165       175       185       195  |    205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365  
                                                                                        77 80                                                                                                                195  |                                                                                                                                                                         
                                                                                                                                                                                                                198                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:352
 aligned with Q67FT0_PSESE | Q67FT0 from UniProtKB/TrEMBL  Length:368

    Alignment length:352
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364  
         Q67FT0_PSESE    15 MQPKDTPELRALYKSFEEESIIPLWTQLGDLMPIHPKSKAVPHVWKWSTLLRLARKSGELVPVGRGGERRALGLANPGLGGNAYISPTMWAGIQYLGPRETAPEHRHSQNAFRFVVEGEGVWTVVNGDPVRMSRGDLLLTPGWCFHGHHNDTDQPMAWIDGLDIPFSQQMDVGFFEFGSDRVTDYATPNFSRGERLWCHPGLRPLSGLQNTVASPIGAYRWEFTDRALTEQLLLEDEGQPATVAPGHAAIRYVNPTTGGDVMPTLRCEFHRLRAGTETATRNEVGSTVFQVFEGAGAVVMNGETTKLEKGDMFVVPSWVPWSLQAETQFDLFRFSDAPIMEALSFMRTKIEG 366
               SCOP domains d2phdd_ D: automated matches                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh..eee.hhh...............eeehhhhhhhhhhhhhhhh.........eeee.hhhhh.........eeeeeee....eeeeeee...eeeeeee.eeeeeee..eeeeee...eeee.....eeeee.....eeeeeeehhhhhhhh....eee.............hhhhhhhh...eee.hhh.........eehhhhhhhhhhhhhhhhhh.........eeeeee.............eeeeeee........eee...eeeeeee.eeeeee..eeeeee...eeee.....eeeee...eeeeeeehhhhhhhh....eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2phd D  15 MQPKDTPELRALYKSFEEESIIPLWTQLGDLMPIHPKSKAVPHVWKWSTLLRLARKSGELVPVGRGGERRALGLANPGLGGNAYISPTMWAGIQYLGPRETAPEHRHSQNAFRFVVEGEGVWTVVNGDPVRMSRGDLLLTPGWCFHGHMNDTDQPMAWIDGLDIPFSQQMDVGFFEFGSDRVTDYATPNFSRGERLWCHPGLRPLSGLQNTVASPIGAYRWEFTDRALTEQLLLEDEGQPATVAPGHAAIRYVNPTTGGDVMPTLRCEFHRLRAGTETATRNEVGSTVFQVFEGAGAVVMNGETTKLEKGDMFVVPSWVPWSLQAETQFDLFRFSDAPIMEALSFMRTKIEG 366
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364
   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  (2, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PHD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PHD)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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

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

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