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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT CHLORITE DISMUTASE FROM CANDIDATUS NITROSPIRA DEFLUVII W146Y R173Q
 
Authors :  K. Gysel, A. Hagmueller, K. Djinovic-Carugo
Date :  01 Aug 13  (Deposition) - 15 Jan 14  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
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
    Fragment: UNP RESIDUES 27-264
    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, 25)

Asymmetric/Biological Unit (4, 25)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
2HEM5Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3IMD2Ligand/IonIMIDAZOLE
4SO49Ligand/IonSULFATE ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:108 , THR A:109 , TYR A:110 , VAL A:111 , ILE A:139 , LYS A:141 , TRP A:145 , MET A:157 , HIS A:160 , THR A:161 , ALA A:164 , GLN A:173 , PHE A:186 , PHE A:190 , LEU A:201 , LEU A:205 , PHE A:217 , IMD A:304 , ARG B:203BINDING SITE FOR RESIDUE HEM A 301
02AC2SOFTWARETHR A:96 , SER A:97 , HOH A:408 , HOH A:428 , GLN B:20 , HIS B:64BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREARG A:93 , ASP B:27BINDING SITE FOR RESIDUE EDO A 303
04AC4SOFTWAREGLN A:173 , LEU A:175 , THR A:188 , PHE A:190 , HEM A:301BINDING SITE FOR RESIDUE IMD A 304
05AC5SOFTWARELYS A:140 , ARG A:215 , ARG A:216 , HIS B:219BINDING SITE FOR RESIDUE SO4 A 305
06AC6SOFTWAREPRO B:108 , THR B:109 , TYR B:110 , VAL B:111 , ILE B:139 , LYS B:141 , TRP B:145 , MET B:157 , HIS B:160 , THR B:161 , ALA B:164 , PHE B:186 , THR B:188 , PHE B:190 , LEU B:205 , PHE B:217 , HOH B:401 , HOH B:418 , HOH B:426BINDING SITE FOR RESIDUE HEM B 301
07AC7SOFTWAREARG B:90 , ARG B:93 , HIS B:94BINDING SITE FOR RESIDUE SO4 B 302
08AC8SOFTWARETYR B:13 , ARG D:194 , LEU D:195 , GLU D:196BINDING SITE FOR RESIDUE SO4 B 303
09AC9SOFTWARELYS B:140 , ARG B:215 , HIS D:219BINDING SITE FOR RESIDUE EDO B 304
10BC1SOFTWAREARG A:203 , PRO C:108 , THR C:109 , TYR C:110 , VAL C:111 , ILE C:139 , TRP C:145 , MET C:157 , HIS C:160 , THR C:161 , ALA C:164 , GLN C:173 , LEU C:175 , PHE C:186 , THR C:188 , PHE C:190 , LEU C:205 , PHE C:217BINDING SITE FOR RESIDUE HEM C 301
11BC2SOFTWAREARG C:194 , LEU C:195 , GLU C:196 , TYR E:13BINDING SITE FOR RESIDUE SO4 C 302
12BC3SOFTWAREHIS A:219 , LYS C:140 , ARG C:215BINDING SITE FOR RESIDUE SO4 C 303
13BC4SOFTWAREARG A:194 , GLU A:196 , TYR C:13BINDING SITE FOR RESIDUE EDO C 304
14BC5SOFTWAREPRO C:115 , GLU C:116 , SER C:117 , HOH C:410BINDING SITE FOR RESIDUE EDO C 305
15BC6SOFTWAREGLN C:173BINDING SITE FOR RESIDUE EDO C 306
16BC7SOFTWAREPRO D:108 , THR D:109 , TYR D:110 , VAL D:111 , ILE D:139 , LYS D:141 , TRP D:145 , MET D:157 , HIS D:160 , THR D:161 , ALA D:164 , LEU D:168 , LEU D:175 , PHE D:186 , THR D:188 , PHE D:190 , LEU D:201 , LEU D:205 , PHE D:217 , IMD D:302 , ARG E:203BINDING SITE FOR RESIDUE HEM D 301
17BC8SOFTWAREGLN D:173 , LYS D:174 , LEU D:175 , PHE D:190 , HEM D:301BINDING SITE FOR RESIDUE IMD D 302
18BC9SOFTWARETYR D:13 , ARG E:194 , LEU E:195 , GLU E:196BINDING SITE FOR RESIDUE SO4 D 303
19CC1SOFTWAREPRO D:115 , GLU D:116 , SER D:117BINDING SITE FOR RESIDUE SO4 D 304
20CC2SOFTWAREASP D:24 , HIS D:94 , HOH D:411BINDING SITE FOR RESIDUE EDO D 305
21CC3SOFTWAREARG C:203 , PRO E:108 , THR E:109 , TYR E:110 , VAL E:111 , ILE E:139 , LYS E:141 , TRP E:145 , MET E:157 , HIS E:160 , THR E:161 , ALA E:164 , LEU E:168 , GLN E:173 , PHE E:186 , PHE E:190 , LEU E:201 , LEU E:205 , PHE E:217 , HOH E:418BINDING SITE FOR RESIDUE HEM E 301
22CC4SOFTWAREGLY E:30BINDING SITE FOR RESIDUE EDO E 302
23CC5SOFTWAREHIS C:219 , LYS E:140 , ARG E:215BINDING SITE FOR RESIDUE EDO E 303
24CC6SOFTWAREPRO E:115 , GLU E:116 , SER E:117BINDING SITE FOR RESIDUE EDO E 304
25CC7SOFTWARELYS D:140 , ARG D:215 , ARG D:216 , HIS E:219BINDING SITE FOR RESIDUE SO4 E 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M09)

(-) 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 4M09)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M09)

(-) Exons   (0, 0)

(no "Exon" information available for 4M09)

(-) 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:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....eeeeeeeee.hhhhh.hhhhhhhhhhhhhhhhhhh....eeeeee.........eeeeeee.hhhhhhhhhhhhhhh.hhh.eeeeeeeeee.....hhhhhhhhhhhhhh.........eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeeee.hhhhhhhhhhhhhh..hhh.eeee....eeeee.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m09 A   1 ADREKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEWYALDQEARTALMQEHTQAALPYLKTVKQKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        


Chain B from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh....eeeeeeeee.hhhhh.hhhhhhhhhhhhhhhhhhh...eeeeeee.........eeeeeee.hhhhhhhhhhhhhhh.hhh.eeeeeeeeee.....hhhhhhhhhhhhhh.........eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee.hhhhhhhhhhhh....hhh.eeee....eeeee.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m09 B   1 ADREKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEWYALDQEARTALMQEHTQAALPYLKTVKQKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        


Chain C from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh....eeeeeeeee.hhhhh.hhhhhhhhhhhhhhhhhhh....eeeeee.........eeeeeee.hhhhhhhhhhhhh...hhh.eeeeeeeeee.....hhhhhhhhhhhhhh.........eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeeee.hhhhhhhhhhhhh...hhh.eeee....eeeee.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m09 C   3 REKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEWYALDQEARTALMQEHTQAALPYLKTVKQKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 238
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232      


Chain D from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh....eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhhhh...eeeeee.........eeeeeee.hhhhhhhhhhhhhhh.hhh.eeeeeeeeee..........hhhhhhhhh.........eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee........eeeeeee.hhhhhhhhhhhhh.hhhhh.eeee....eeee..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m09 D   3 REKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEWYALDQEARTALMQEHTQAALPYLKTVKQKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 238
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232      


Chain E from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeee.hhhhh.hhhhhhhhhhhhhhhhhhh...eeeeeee.........eeeeeee.hhhhhhhhhhhhhhh.hhh.eeeeeeeeee.....hhhhhhhhhhhhhh.........eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeeee.hhhhhhhhhhhhhh..hhh.eeee....eeeee.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m09 E   2 DREKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEWYALDQEARTALMQEHTQAALPYLKTVKQKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
   Legend:   → Mismatch (orange background)
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    → 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 4M09)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M09)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M09)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        B3U4H7_9BACT | B3U4H7: 3nn1 3nn2 3nn3 3nn4 4m05 4m06 4m07 4m08

(-) Related Entries Specified in the PDB File

4m05 4m06 4m07 4m08