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(-) Description

Title :  STRUCTURE OF Y257F VARIANT OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-NITROCATECHOL AND DIOXYGEN AT 1.67 ANG RESOLUTION
 
Authors :  E. G. Kovaleva, J. D. Lipscomb
Date :  07 Aug 12  (Deposition) - 31 Oct 12  (Release) - 12 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dioxygenase, Oxygen Activation, Fe(Ii), 2-His-1-Carboxylate Facial Triad, Homoprotocatechuate, 4-Nitrocatechol, Oxy Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. G. Kovaleva, J. D. Lipscomb
Structural Basis For The Role Of Tyrosine 257 Of Homoprotocatechuate 2, 3-Dioxygenase In Substrate And Oxygen Activation.
Biochemistry V. 51 8755 2012
PubMed-ID: 23066739  |  Reference-DOI: 10.1021/BI301115C

(-) Compounds

Molecule 1 - HOMOPROTOCATECHUATE 2,3-DIOXYGENASE
    Chains: A, B, C, D
    EC Number: 1.13.11.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PYZW204
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HPCD
    Mutation: YES
    Organism Scientific: BREVIBACTERIUM FUSCUM
    Organism Taxid: 47914
    Strain: ATCC 15993

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 21)

Asymmetric/Biological Unit (7, 21)
No.NameCountTypeFull Name
14NC3Ligand/Ion4-NITROCATECHOL
2CA1Ligand/IonCALCIUM ION
3CL4Ligand/IonCHLORIDE ION
4FE24Ligand/IonFE (II) ION
5OXY2Ligand/IonOXYGEN MOLECULE
6P6G5Ligand/IonHEXAETHYLENE GLYCOL
7PG42Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:155 , HIS A:214 , GLU A:267 , 4NC A:402 , HOH A:682BINDING SITE FOR RESIDUE FE2 A 401
02AC2SOFTWAREHIS A:155 , TRP A:192 , HIS A:200 , HIS A:214 , ARG A:243 , HIS A:248 , VAL A:250 , SER A:251 , PHE A:257 , GLU A:267 , TYR A:269 , ARG A:292 , ARG A:293 , FE2 A:401 , CL A:404 , HOH A:682BINDING SITE FOR RESIDUE 4NC A 402
03AC3SOFTWAREGLU A:22 , LYS A:68 , LYS A:75 , ARG A:104 , PHE A:108 , ASP A:315 , GLY A:316BINDING SITE FOR RESIDUE P6G A 403
04AC4SOFTWAREARG A:243 , HIS A:248 , ARG A:293 , 4NC A:402BINDING SITE FOR RESIDUE CL A 404
05AC5SOFTWAREHIS B:155 , HIS B:214 , GLU B:267 , HOH B:738 , HOH B:795 , HOH B:796BINDING SITE FOR RESIDUE FE2 B 401
06AC6SOFTWAREARG B:243 , HIS B:248 , ARG B:293BINDING SITE FOR RESIDUE CL B 402
07AC7SOFTWAREASP A:184 , GLU A:185 , HOH A:632 , ASP B:184 , GLU B:185 , HOH B:501BINDING SITE FOR RESIDUE CA B 403
08AC8SOFTWAREARG A:82 , ALA B:12 , ASP B:172 , GLY B:174 , ARG B:195 , HOH B:760 , HOH B:792BINDING SITE FOR RESIDUE PG4 B 404
09AC9SOFTWAREGLU B:22 , THR B:67 , LYS B:75 , ARG B:104 , PHE B:108 , ASP B:315 , GLY B:316 , HOH B:719BINDING SITE FOR RESIDUE P6G B 405
10BC1SOFTWAREASP A:183 , ASP A:184 , THR A:284 , ALA A:344 , GLY A:345 , HOH A:667 , ALA B:344 , GLY B:345 , HOH B:564 , HOH B:736 , HOH B:752 , HOH B:754BINDING SITE FOR RESIDUE P6G B 406
11BC2SOFTWAREHIS C:155 , HIS C:214 , GLU C:267 , 4NC C:402 , OXY C:405 , HOH C:792BINDING SITE FOR RESIDUE FE2 C 401
12BC3SOFTWAREHIS C:155 , TRP C:192 , HIS C:200 , HIS C:214 , ARG C:243 , HIS C:248 , VAL C:250 , SER C:251 , PHE C:257 , GLU C:267 , TYR C:269 , ARG C:292 , ARG C:293 , FE2 C:401 , OXY C:405 , CL C:406 , HOH C:792BINDING SITE FOR RESIDUE 4NC C 402
13BC4SOFTWAREALA C:12 , GLY C:174 , ARG C:195 , HOH C:786 , ARG D:82BINDING SITE FOR RESIDUE PG4 C 403
14BC5SOFTWAREGLU C:22 , LYS C:68 , LYS C:75 , ARG C:104 , PHE C:108 , ASP C:315 , GLY C:316 , HOH C:690BINDING SITE FOR RESIDUE P6G C 404
15BC6SOFTWAREHIS C:155 , ASN C:157 , TRP C:192 , HIS C:200 , ALA C:203 , HIS C:214 , FE2 C:401 , 4NC C:402 , HOH C:792BINDING SITE FOR RESIDUE OXY C 405
16BC7SOFTWAREARG C:243 , HIS C:248 , ARG C:293 , TRP C:304 , 4NC C:402BINDING SITE FOR RESIDUE CL C 406
17BC8SOFTWAREHIS D:155 , HIS D:200 , HIS D:214 , GLU D:267 , 4NC D:402 , OXY D:404 , HOH D:812BINDING SITE FOR RESIDUE FE2 D 401
18BC9SOFTWAREHIS D:155 , TRP D:192 , HIS D:200 , HIS D:214 , ARG D:243 , HIS D:248 , VAL D:250 , SER D:251 , PHE D:257 , GLU D:267 , TYR D:269 , ARG D:292 , ARG D:293 , FE2 D:401 , OXY D:404 , CL D:405 , HOH D:812BINDING SITE FOR RESIDUE 4NC D 402
19CC1SOFTWAREGLU 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:719BINDING SITE FOR RESIDUE P6G D 403
20CC2SOFTWAREHIS D:155 , ASN D:157 , TRP D:192 , HIS D:200 , ALA D:203 , HIS D:214 , FE2 D:401 , 4NC D:402 , HOH D:812BINDING SITE FOR RESIDUE OXY D 404
21CC3SOFTWAREARG D:243 , HIS D:248 , ARG D:293 , 4NC D:402BINDING SITE FOR RESIDUE CL D 405

(-) SS Bonds  (0, 0)

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

(-) 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 4GHF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GHF)

(-) 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....................hhhhhhhh...ee..........ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ghf A   4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLFILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQASKG 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......eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ghf B   4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLFILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQASKGFKLG 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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeee.hhhhhhhhhhh....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
                 4ghf C   4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLFILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQ 354
                                    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.................hhhhhhh....ee..........ee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ghf D   4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLFILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEIIERTDDSELEVTIGADGFSFTRAGDEDGSYHGQASKGFKLG 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 4GHF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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        Q45135_9MICO | Q45135: 1f1x 1q0c 1q0o 2ig9 2iga 3bza 3ecj 3eck 3ojj 3ojk 3ojn 3ojt 4ghc 4ghd 4ghe 4ghg 4ghh 4z6l 4z6m 4z6n 4z6o 4z6p 4z6q 4z6r 4z6s 4z6t 4z6u 4z6v 4z6w 4z6z 5bwg 5bwh 5trx

(-) Related Entries Specified in the PDB File

4ghc STRUCTURE OF Y257F VARIANT OF HOMOPROTOCATECHUATE 2,3- DIOXYGENASE FROM B.FUSCUM AT 1.55 ANG RESOLUTION
4ghd STRUCTURE OF Y257F VARIANT OF HOMOPROTOCATECHUATE 2,3- DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH HPCA AT 1.85 ANG RESOLUTION
4ghe STRUCTURE OF Y257F VARIANT OF HOMOPROTOCATECHUATE 2,3- DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-NITROCATECHOL AT 1.60 ANG RESOLUTION
4ghg STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH HPCA AT 1.50 ANG RESOLUTION
4ghh STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM B.FUSCUM IN COMPLEX WITH 4-NITROCATECHOL AT 1.55 ANG RESOLUTION