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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT CHLORITE DISMUTASE FROM CANDIDATUS NITROSPIRA DEFLUVII W145V
 
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 :  2.80
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, 42)

Asymmetric/Biological Unit (4, 42)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2HEM5Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3IMD5Ligand/IonIMIDAZOLE
4SO422Ligand/IonSULFATE ION

(-) Sites  (42, 42)

Asymmetric Unit (42, 42)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:108 , THR A:109 , TYR A:110 , VAL A:111 , PHE A:114 , LEU A:122 , MET A:157 , HIS A:160 , THR A:161 , ALA A:164 , LEU A:168 , ARG A:173 , PHE A:186 , PHE A:190 , LEU A:201 , LEU A:205 , IMD A:306 , EDO A:310 , HOH A:407 , HOH A:421BINDING SITE FOR RESIDUE HEM A 301
02AC2SOFTWAREHIS A:199 , ARG A:203 , LYS E:106 , HIS E:177BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREPRO A:29 , GLY A:30 , ARG A:33BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWAREPRO A:228 , LEU A:229 , HOH A:402 , HOH A:414BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWAREARG A:90 , HOH A:417 , SER B:117BINDING SITE FOR RESIDUE SO4 A 305
06AC6SOFTWAREGLU A:193 , ARG A:194 , LEU A:195 , GLU A:196 , TYR E:13BINDING SITE FOR RESIDUE SO4 A 311
07AC7SOFTWARELYS A:174 , LEU A:175 , HEM A:301 , SO4 A:309 , EDO A:310BINDING SITE FOR RESIDUE IMD A 306
08AC8SOFTWAREGLN A:150 , GLU B:151BINDING SITE FOR RESIDUE EDO A 307
09AC9SOFTWARELYS A:106 , HIS A:177 , HOH A:403 , HIS C:199 , ARG C:203BINDING SITE FOR RESIDUE SO4 A 308
10BC1SOFTWARELYS A:174 , LEU A:175 , IMD A:306 , EDO A:310 , HOH A:409BINDING SITE FOR RESIDUE SO4 A 309
11BC2SOFTWAREARG A:173 , HEM A:301 , IMD A:306 , SO4 A:309BINDING SITE FOR RESIDUE EDO A 310
12BC3SOFTWAREPRO B:108 , THR B:109 , TYR B:110 , VAL B:111 , ILE B:137 , ILE B:139 , MET B:157 , HIS B:160 , THR B:161 , ALA B:164 , TYR B:167 , ARG B:173 , PHE B:186 , PHE B:190 , LEU B:201 , LEU B:205 , PHE B:217 , IMD B:305BINDING SITE FOR RESIDUE HEM B 301
13BC4SOFTWAREHIS B:199 , ARG B:203 , HOH B:423 , LYS C:106 , HIS C:177BINDING SITE FOR RESIDUE SO4 B 302
14BC5SOFTWAREARG B:194 , LEU B:195 , TYR C:13BINDING SITE FOR RESIDUE SO4 B 309
15BC6SOFTWARELEU B:175 , IMD B:305 , HOH B:409BINDING SITE FOR RESIDUE SO4 B 303
16BC7SOFTWAREGLU B:159 , GLN B:207 , ALA C:147BINDING SITE FOR RESIDUE EDO B 304
17BC8SOFTWARELYS B:140BINDING SITE FOR RESIDUE EDO B 310
18BC9SOFTWAREARG B:173 , LYS B:174 , LEU B:175 , HEM B:301 , SO4 B:303BINDING SITE FOR RESIDUE IMD B 305
19CC1SOFTWAREGLU B:116BINDING SITE FOR RESIDUE EDO B 306
20CC2SOFTWAREHIS B:23 , ASP B:24BINDING SITE FOR RESIDUE EDO B 307
21CC3SOFTWAREGLU A:151 , GLN B:150 , ARG B:153 , HOH B:416BINDING SITE FOR RESIDUE SO4 B 308
22CC4SOFTWAREPRO C:108 , THR C:109 , TYR C:110 , VAL C:111 , LEU C:122 , LYS C:141 , HIS C:160 , THR C:161 , ALA C:164 , LEU C:168 , ARG C:173 , PHE C:186 , PHE C:190 , LEU C:205 , PHE C:217 , IMD C:305 , HOH C:408 , HOH C:416BINDING SITE FOR RESIDUE HEM C 302
23CC5SOFTWAREGLN B:207 , ASP C:149 , GLN C:150 , GLU C:151 , ARG C:153BINDING SITE FOR RESIDUE SO4 C 303
24CC6SOFTWAREPRO C:29 , GLY C:30 , GLN C:162BINDING SITE FOR RESIDUE SO4 C 304
25CC7SOFTWAREARG C:173 , LYS C:174 , LEU C:175 , HEM C:302 , SO4 C:306BINDING SITE FOR RESIDUE IMD C 305
26CC8SOFTWARELYS C:174 , LEU C:175 , IMD C:305 , HOH C:412 , HOH C:423BINDING SITE FOR RESIDUE SO4 C 306
27CC9SOFTWARETYR A:13 , GLU C:193 , ARG C:194 , LEU C:195 , GLU C:196 , HOH C:426 , HOH C:432BINDING SITE FOR RESIDUE SO4 C 307
28DC1SOFTWARETYR D:13 , ARG D:74 , ARG E:194 , LEU E:195 , GLU E:196BINDING SITE FOR RESIDUE SO4 D 305
29DC2SOFTWAREGLU C:39 , GLY C:88 , ARG C:90 , ARG C:93 , LYS C:169BINDING SITE FOR RESIDUE SO4 C 308
30DC3SOFTWAREPRO C:115 , GLU C:116 , SER C:117 , HOH C:405BINDING SITE FOR RESIDUE SO4 C 309
31DC4SOFTWAREHIS B:219 , LYS C:140 , ARG C:215BINDING SITE FOR RESIDUE EDO C 301
32DC5SOFTWAREGLU C:31 , GLN C:162BINDING SITE FOR RESIDUE EDO C 310
33DC6SOFTWARELYS D:140 , ARG E:215 , ARG E:216 , PHE E:217 , HIS E:219BINDING SITE FOR RESIDUE EDO E 305
34DC7SOFTWAREPRO D:108 , THR D:109 , TYR D:110 , VAL D:111 , LEU D:122 , ILE D:139 , TRP D:146 , HIS D:160 , THR D:161 , ALA D:164 , LEU D:168 , ARG D:173 , PHE D:186 , PHE D:190 , LEU D:205 , IMD D:304BINDING SITE FOR RESIDUE HEM D 301
35DC8SOFTWAREARG A:215 , ARG A:216 , HIS A:219 , LYS E:140BINDING SITE FOR RESIDUE EDO E 306
36DC9SOFTWARELYS D:174 , LEU D:175 , IMD D:304BINDING SITE FOR RESIDUE SO4 D 302
37EC1SOFTWARETYR B:13 , GLU D:193 , ARG D:194 , LEU D:195 , GLU D:196BINDING SITE FOR RESIDUE SO4 D 303
38EC2SOFTWAREARG D:173 , LYS D:174 , HEM D:301 , SO4 D:302BINDING SITE FOR RESIDUE IMD D 304
39EC3SOFTWAREPRO E:108 , THR E:109 , TYR E:110 , VAL E:111 , LEU E:122 , ILE E:139 , 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 , IMD E:304BINDING SITE FOR RESIDUE HEM E 301
40EC4SOFTWAREARG E:173 , LYS E:174 , LEU E:175 , IMD E:304 , HOH E:404BINDING SITE FOR RESIDUE SO4 E 302
41EC5SOFTWAREPRO E:228 , LEU E:229BINDING SITE FOR RESIDUE SO4 E 303
42EC6SOFTWAREARG E:173 , LYS E:174 , LEU E:175 , HEM E:301 , SO4 E:302BINDING SITE FOR RESIDUE IMD E 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M08)

(-) 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 4M08)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M08)

(-) Exons   (0, 0)

(no "Exon" information available for 4M08)

(-) 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.hhhh..hhhhhhhhhhhhhhhhhhh....eeeeee.........eeeeeee.hhhhhhhhhhhhh...hhh.eeeeeeeeee.....hhhhhhhhhhhhh..........eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhh.eeee....eeeee.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m08 A   1 ADREKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEVWALDQEARTALMQEHTQAALPYLKTVKRKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 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.hhhh..hhhhhhhhhhhhhhhhhhh...eeeeeee.........eeeeeee.hhhhhhhhhhhhh.hhhhhheeeeeeeeee.....hhhhhhhhhhhhh..........eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhh.eeee....eeeee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m08 B   1 ADREKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEVWALDQEARTALMQEHTQAALPYLKTVKRKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 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:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhhh....eeeeee.........eeeeeee.hhhhhhhhhhhhh.hhhhhheeeeeeeeee.....hhhhhhhhhhhhh..........eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhh.eeee....eeeee.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m08 C   1 ADREKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEVWALDQEARTALMQEHTQAALPYLKTVKRKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 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 D from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.....eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhhh....eeeeee.........eeeeeee.hhhhhhhhhhhhh.hhhhhheeeeeeeeee.....hhhhhhhhhhhhh..........eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhh.eeee....eeeee.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m08 D   1 ADREKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEVWALDQEARTALMQEHTQAALPYLKTVKRKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 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 E from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.....eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhhh...eeeeeee.........eeeeeee.hhhhhhhhhhhhh...hhh.eeeeeeeeee.....hhhhhhhhhhhhh..........eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee........eeeeeee.hhhhhhhhhhhhhhhhhhh.eeee....eeeee.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m08 E   1 ADREKLLTESGVYGTFATFQMDHDWWDLPGESRVISVAEVKGLVEQWSGKILVESYLLRGLSDHADLMFRVHARTLSDTQQFLSAFMGTRLGRHLTSGGLLHGVSKKPTYVAGFPESMKTELQVNGESGSRPYAIVIPIKKDAEVWALDQEARTALMQEHTQAALPYLKTVKRKLYHSTGLDDVDFITYFETERLEDFHNLVRALQQVKEFRHNRRFGHPTLLGTMSPLDEILEKFAQ 238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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 4M08)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M08)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M08)

(-) Gene Ontology  (4, 4)

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  4m08
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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 4m09

(-) Related Entries Specified in the PDB File

4m05 4m06 4m07 4m09