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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT CHLORITE DISMUTASE FROM CANDIDATUS NITROSPIRA DEFLUVII W145F IN COMPLEX WITH CYANIDE
 
Authors :  A. Hagmueller, K. Gysel, K. Djinovic-Carugo
Date :  01 Aug 13  (Deposition) - 15 Jan 14  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Ferredoxin-Like Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Hofbauer, K. Gysel, M. Bellei, A. Hagmuller, I. Schaffner, G. Mlynek, J. Kostan, K. F. Pirker, H. Daims, P. G. Furtmuller, G. Battistuzzi, K. Djinovic-Carugo, C. Obinger
Manipulating Conserved Heme Cavity Residues Of Chlorite Dismutase: Effect On Structure, Redox Chemistry, And Reactivity.
Biochemistry V. 53 77 2014
PubMed-ID: 24364531  |  Reference-DOI: 10.1021/BI401042Z

(-) Compounds

Molecule 1 - CHLORITE DISMUTASE
    Chains: A, B, C, D, E
    EC Number: 1.13.11.49
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B STREP TEV
    Expression System Strain: BL21(DE3) TUNER
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CLD, CLD1, NIDE1387
    Mutation: YES
    Organism Scientific: CANDIDATUS NITROSPIRA DEFLUVII
    Organism Taxid: 330214

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1CYN5Ligand/IonCYANIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4HEM5Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:108 , THR A:109 , TYR A:110 , VAL A:111 , ILE A:139 , PHE A:145 , MET A:157 , HIS A:160 , THR A:161 , ALA A:164 , LEU A:168 , ARG A:173 , LEU A:175 , PHE A:186 , THR A:188 , PHE A:190 , LEU A:201 , LEU A:205 , PHE A:217 , CYN A:303BINDING SITE FOR RESIDUE HEM A 301
02AC2SOFTWARELYS A:140 , ARG C:215 , ARG C:216 , PHE C:217 , HIS C:219BINDING SITE FOR RESIDUE GOL A 302
03AC3SOFTWARELEU A:175 , HEM A:301BINDING SITE FOR RESIDUE CYN A 303
04AC4SOFTWAREPRO B:108 , THR B:109 , TYR B:110 , LEU B:122 , ILE B:137 , ILE B:139 , PHE B:145 , MET B:157 , HIS B:160 , THR B:161 , ALA B:164 , LEU B:168 , ARG B:173 , LEU B:175 , PHE B:186 , THR B:188 , PHE B:190 , LEU B:205 , PHE B:217 , CYN B:302BINDING SITE FOR RESIDUE HEM B 301
05AC5SOFTWARELEU B:175 , HEM B:301BINDING SITE FOR RESIDUE CYN B 302
06AC6SOFTWAREPRO C:108 , THR C:109 , TYR C:110 , VAL C:111 , ILE C:139 , HIS C:160 , THR C:161 , ALA C:164 , LEU C:168 , ARG C:173 , LEU C:175 , PHE C:186 , THR C:188 , PHE C:190 , LEU C:201 , LEU C:205 , PHE C:217 , CYN C:302 , HOH C:403BINDING SITE FOR RESIDUE HEM C 301
07AC7SOFTWAREHEM C:301BINDING SITE FOR RESIDUE CYN C 302
08AC8SOFTWAREARG C:173BINDING SITE FOR RESIDUE EDO C 303
09AC9SOFTWAREPRO D:108 , THR D:109 , TYR D:110 , VAL D:111 , ILE D:139 , PHE D:145 , MET D:157 , HIS D:160 , THR D:161 , ALA D:164 , ARG D:173 , PHE D:186 , THR D:188 , PHE D:190 , LEU D:205 , PHE D:217 , CYN D:302BINDING SITE FOR RESIDUE HEM D 301
10BC1SOFTWAREHEM D:301BINDING SITE FOR RESIDUE CYN D 302
11BC2SOFTWAREPRO E:108 , THR E:109 , TYR E:110 , VAL E:111 , LEU E:122 , ILE E:137 , ILE E:139 , PHE E:145 , MET E:157 , HIS E:160 , THR E:161 , ALA E:164 , LEU E:168 , ARG E:173 , LEU E:175 , PHE E:186 , PHE E:190 , LEU E:205 , PHE E:217 , CYN E:302BINDING SITE FOR RESIDUE HEM E 301
12BC3SOFTWAREHEM E:301BINDING SITE FOR RESIDUE CYN E 302
13BC4SOFTWARELEU D:100 , LEU D:181 , LEU E:61 , SER E:62 , ASP E:63 , THR E:221BINDING SITE FOR RESIDUE EDO E 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M06)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1His A:219 -Pro A:220
2His B:219 -Pro B:220
3His C:219 -Pro C:220
4His D:219 -Pro D:220
5His E:219 -Pro E:220

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M06)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M06)

(-) Exons   (0, 0)

(no "Exon" information available for 4M06)

(-) 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:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh...eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.........eeeeeee.hhhhhhhhhhhhh...hhh.eeeeeeeeee.....hhhhhhhhhhhhh..........eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhh.eeee....eeeee.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m06 A   4 EKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEFWALDQEARTALMQEHTQAALPYLKTVKRKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 238
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233     


Chain B from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh...eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.........eeeeeee.hhhhhhhhhhhhh...hhh.eeeeeeeeee.....hhhhhhhhhhhhh..........eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhh.eeee....eeeee.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m06 B   0 MADREKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEFWALDQEARTALMQEHTQAALPYLKTVKRKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 238
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229         


Chain C from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh...eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhhhh...eeeeee.........eeeeeee.hhhhhhhhhhhhhhh.hhh.eeeeeeeeee.....hhhhhhhhhhhhh..........eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhh.eeee....eeeee.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m06 C   2 DREKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEFWALDQEARTALMQEHTQAALPYLKTVKRKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       


Chain D from PDB  Type:PROTEIN  Length:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhhhh...eeeeee.........eeeeeee.hhhhhhhhhhhhhhh.hhh.eeeeeeeeee.....hhhhhhhhhhhhh..........eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhh.eeee....eeeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m06 D   4 EKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEFWALDQEARTALMQEHTQAALPYLKTVKRKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 238
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233     


Chain E from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh...eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.........eeeeeee.hhhhhhhhhhhhhhh.hhh.eeeeeeeeee.....hhhhhhhhhhhhh..........eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhh.eeee....eeeee.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m06 E   0 MADREKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEFWALDQEARTALMQEHTQAALPYLKTVKRKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 238
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229
   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  (0, 0)

(no "SCOP Domain" information available for 4M06)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M06)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M06)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        B3U4H7_9BACT | B3U4H7: 3nn1 3nn2 3nn3 3nn4 4m05 4m07 4m08 4m09

(-) Related Entries Specified in the PDB File

4m05 4m07 4m08 4m09