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(-) Description

Title :  STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-SULFONYL CATECHOL AT 1.52 ANG RESOLUTION
 
Authors :  E. G. Kovaleva, J. D. Lipscomb
Date :  06 Apr 15  (Deposition) - 26 Aug 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.52
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dioxygenase, 2-His-1-Carboxylate Facial Triad, Oxygen Activation, Acid-Base Catalysis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. G. Kovaleva, M. S. Rogers, J. D. Lipscomb
Structural Basis For Substrate And Oxygen Activation In Homoprotocatechuate 2, 3-Dioxygenase: Roles Of Conserved Active Site Histidine 200.
Biochemistry V. 54 5329 2015
PubMed-ID: 26267790  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00709

(-) Compounds

Molecule 1 - HOMOPROTOCATECHUATE 2,3-DIOXYGENASE
    Atcc: 15993
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PYZW204
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BREVIBACTERIUM FUSCUM
    Organism Taxid: 47914

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 19)

Asymmetric/Biological Unit (7, 19)
No.NameCountTypeFull Name
14SX2Ligand/Ion3,4-DIHYDROXYBENZENESULFONIC ACID
2CA1Ligand/IonCALCIUM ION
3CL4Ligand/IonCHLORIDE ION
4FE24Ligand/IonFE (II) ION
5MPO2Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID
6P6G5Ligand/IonHEXAETHYLENE GLYCOL
7PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:155 , HIS A:214 , GLU A:267 , HOH A:501 , HOH A:635 , HOH A:728binding site for residue FE2 A 401
02AC2SOFTWAREGLU A:22 , LYS A:68 , LYS A:75 , PHE A:108 , ASP A:315 , GLY A:316 , HOH A:569binding site for residue P6G A 402
03AC3SOFTWAREARG A:243 , HIS A:248 , ARG A:293binding site for residue CL A 403
04AC4SOFTWAREILE A:283 , TRP A:285 , ARG A:343 , ALA A:344 , HOH A:515 , HOH A:632 , HOH A:638 , HOH A:713 , HOH B:858 , ARG C:236binding site for residue MPO A 404
05AC5SOFTWAREHIS B:155 , HIS B:214 , GLU B:267 , HOH B:507 , HOH B:624 , HOH B:709binding site for residue FE2 B 401
06AC6SOFTWAREASP A:184 , GLU A:185 , HOH A:699 , ASP B:184 , GLU B:185 , HOH B:737binding site for residue CA B 402
07AC7SOFTWAREGLU B:22 , LYS B:68 , LYS B:75 , ARG B:104 , PHE B:108 , ASP B:315 , GLY B:316 , HOH B:623binding site for residue P6G B 403
08AC8SOFTWAREGLN A:182 , ASP A:183 , THR A:284 , ALA A:344 , GLY A:345 , HOH A:717 , ASP B:183 , THR B:284 , ALA B:344 , GLY B:345 , HOH B:552 , HOH B:642 , HOH B:766binding site for residue P6G B 404
09AC9SOFTWAREARG B:243 , HIS B:248 , ARG B:293binding site for residue CL B 405
10AD1SOFTWAREILE B:283 , TRP B:285 , ASP B:289 , ARG B:343 , ALA B:344 , HOH B:502 , HOH B:568 , HOH B:595 , HOH B:677 , HOH B:722 , ARG D:236binding site for residue MPO B 406
11AD2SOFTWAREHIS C:155 , HIS C:214 , GLU C:267 , 4SX C:403 , HOH C:644binding site for residue FE2 C 401
12AD3SOFTWAREGLU C:22 , LYS C:68 , LYS C:75 , ARG C:104 , PHE C:108 , ASP C:315 , GLY C:316 , HOH C:636 , HOH C:762binding site for residue P6G C 402
13AD4SOFTWAREHIS C:155 , TRP C:192 , HIS C:200 , HIS C:214 , ARG C:243 , HIS C:248 , VAL C:250 , SER C:251 , TYR C:257 , GLU C:267 , TYR C:269 , ARG C:292 , ARG C:293 , FE2 C:401 , CL C:404 , HOH C:644binding site for residue 4SX C 403
14AD5SOFTWAREARG C:243 , HIS C:248 , ARG C:293 , 4SX C:403binding site for residue CL C 404
15AD6SOFTWAREHIS D:155 , HIS D:214 , GLU D:267 , 4SX D:403 , HOH D:643 , HOH D:688binding site for residue FE2 D 401
16AD7SOFTWAREGLU D:22 , THR D:67 , LYS D:68 , LYS D:75 , ARG D:104 , PHE D:108 , ASP D:315 , GLY D:316 , HOH D:603binding site for residue P6G D 402
17AD8SOFTWAREHIS D:155 , TRP D:192 , HIS D:200 , HIS D:214 , ARG D:243 , HIS D:248 , VAL D:250 , SER D:251 , TYR D:257 , GLU D:267 , TYR D:269 , ARG D:292 , ARG D:293 , FE2 D:401 , CL D:404 , HOH D:643 , HOH D:688 , HOH D:770binding site for residue 4SX D 403
18AD9SOFTWAREARG D:243 , HIS D:248 , ARG D:293 , 4SX D:403binding site for residue CL D 404
19AE1SOFTWAREASN C:208 , ILE C:321 , GLU C:323 , TYR D:45 , ASP D:106 , LYS D:110 , THR D:133 , HOH D:517binding site for residue PG4 D 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z6Z)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gly A:209 -Pro A:210
2Gly A:244 -Pro A:245
3Gly B:209 -Pro B:210
4Gly B:244 -Pro B:245
5Gly C:209 -Pro C:210
6Gly C:244 -Pro C:245
7Gly D:209 -Pro D:210
8Gly D:244 -Pro D:245

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z6Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z6Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z6Z)

(-) 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:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeee.hhhhhhhhhh.....eeeee...eeeee.........eeeee....eeeeeeeee.hhhhhhhhhhhhhhh...eeee..........eeeee.....eeeee......................eeeeeeeee.hhhhhhhhhhhh..eeeeeee.....eeeeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh.hhh.eeeeeee......eeeeee.....eeeeee............eeee..............hhhhhhh....................hhhhhhh....ee..........ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z6z A   4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQASKG 358
                                    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     


Chain B from PDB  Type:PROTEIN  Length:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeee.hhhhhhhhhh.....eeeee...eeeee.........eeeee....eeeeeeeee.hhhhhhhhhhhhhhh...eeee..........eeeee.....eeeee......................eeeeeeeee.hhhhhhhhhhhh..eeeeeee.....eeeeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh.hhh.eeeeeee......eeeeee.....eeeeee............eeee..............hhhhhhh.ee.................hhhhhhh....ee..........ee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z6z B   4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQASKGFKLG 362
                                    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         


Chain C from PDB  Type:PROTEIN  Length:354
                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeeeeeeeeee.hhhhhhhhhh.....eeeee...eeeee.........eeeee....eeeeeeeee..hhhhhhhhhhhhhh...eeee..........eeeee.....eeeee......................eeeeeeeee.hhhhhhhhhhhh..eeeeeee.....eeeeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh.hhh.eeeeeee......eeeeee.....eeeeee............eeee..............hhhhhhh.ee.................hhhhhhh....ee..........ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4z6z C   4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQASK 357
                                    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    


Chain D from PDB  Type:PROTEIN  Length:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeee.hhhhhhhhhh.....eeeee...eeeee.........eeeee....eeeeeeeee.hhhhhhhhhhhhhhh...eeee..........eeeee.....eeeee......................eeeeeeeee.hhhhhhhhhhhh..eeeeeee.....eeeeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh.hhh.eeeeeee......eeeeee.....eeeeee............eeee..............hhhhhhh.ee.................hhhhhhhh...ee..........ee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z6z D   4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQASKGFKLG 362
                                    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
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 4Z6Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z6Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z6Z)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q45135_9MICO | Q45135: 1f1x 1q0c 1q0o 2ig9 2iga 3bza 3ecj 3eck 3ojj 3ojk 3ojn 3ojt 4ghc 4ghd 4ghe 4ghf 4ghg 4ghh 4z6l 4z6m 4z6n 4z6o 4z6p 4z6q 4z6r 4z6s 4z6t 4z6u 4z6v 4z6w 5bwg 5bwh 5trx

(-) Related Entries Specified in the PDB File

4z6l STRUCTURE OF H200E VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM AT 1.65 ANG RESOLUTION
4z6m STRUCTURE OF H200Q VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM AT 1.35 ANG RESOLUTION
4z6n STRUCTURE OF H200N VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM AT 1.52 ANG RESOLUTION
4z6o STRUCTURE OF H200E VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH HPCA AT 1.63 ANG RESOLUTION
4z6p STRUCTURE OF H200Q VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH HPCA AT 1.75 ANG RESOLUTION
4z6q STRUCTURE OF H200N VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH HPCA AT 1.57 ANG RESOLUTION
4z6r STRUCTURE OF H200E VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-SULFONYL CATECHOL AT 1.70 ANG RESOLUTION
4z6s STRUCTURE OF H200Q VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-SULFONYL CATECHOL AT 1.42 ANG RESOLUTION
4z6t STRUCTURE OF H200N VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-SULFONYL CATECHOL AT 1.50 ANG RESOLUTION
4z6u STRUCTURE OF H200E VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-NITROCATECHOL AT 1.48 ANG RESOLUTION
4z6v STRUCTURE OF H200Q VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-NITROCATECHOL AT 1.37 ANG RESOLUTION
4z6w STRUCTURE OF H200N VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-NITROCATECHOL AT 1.57 ANG RESOLUTION