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(-) Description

Title :  CRYSTAL STRUCTURES OF FERRITIN MUTANTS REVEAL DIFERRIC-PEROXO INTERMEDIATES
 
Authors :  S. Kim, Y. H. Park, S. W. Jung, J. H. Seok, Y. B. Chung, D. B. Lee, G. Gowda, J H. R. Han, A. E. Cho, C. Lee, M. S. Chung, K. H. Kim
Date :  15 May 15  (Deposition) - 15 Jun 16  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (4x)
Keywords :  Helicobactor Pylori, Escherichia Coli, Gram-Negative Bacteria, Ferritin, Iron Uptake, Ferroxidase Center, Reaction Intermediate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kim, J. H. Lee, J. H. Seok, Y. H. Park, S. W. Jung, A. E. Cho, C. Lee, M. S. Chung, K. H. Kim
Structural Basis Of Novel Iron-Uptake Route And Reaction Intermediates In Ferritins From Gram-Negative Bacteria.
J. Mol. Biol. V. 428 5007 2016
PubMed-ID: 27777002  |  Reference-DOI: 10.1016/J.JMB.2016.10.022

(-) Compounds

Molecule 1 - BACTERIAL NON-HEME FERRITIN
    Chains: A, B, C, D, E, F
    EC Number: 1.16.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Taxid: 866768
    Gene: FTNA, Z2960, ECS2613
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI DH1
    Organism Taxid: 536056
    Synonym: FERRITIN-1

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (4x): ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 37)

Asymmetric Unit (8, 37)
No.NameCountTypeFull Name
2FE5Ligand/IonFE (III) ION
1FE22Ligand/IonFE (II) ION
3FEO3Ligand/IonMU-OXO-DIIRON
4GOL14Ligand/IonGLYCEROL
5O2Ligand/IonOXYGEN ATOM
6OH9Ligand/IonHYDROXIDE ION
7OXY1Ligand/IonOXYGEN MOLECULE
8PER1Ligand/IonPEROXIDE ION
Biological Unit 1 (5, 84)
No.NameCountTypeFull Name
2FE-1Ligand/IonFE (III) ION
1FE28Ligand/IonFE (II) ION
3FEO12Ligand/IonMU-OXO-DIIRON
4GOL56Ligand/IonGLYCEROL
5O-1Ligand/IonOXYGEN ATOM
6OH-1Ligand/IonHYDROXIDE ION
7OXY4Ligand/IonOXYGEN MOLECULE
8PER4Ligand/IonPEROXIDE ION

(-) Sites  (37, 37)

Asymmetric Unit (37, 37)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:17 , GLU A:50 , HIS A:53 , GLU A:94 , GLN A:127 , GLU A:130 , OH A:202 , OH A:203 , HOH A:301binding site for residue FEO A 201
02AC2SOFTWAREGLU A:17 , HIS A:53 , TYR A:123 , GLN A:127 , FEO A:201 , OH A:203binding site for residue OH A 202
03AC3SOFTWAREGLU A:17 , GLU A:50 , ILE A:97 , FEO A:201 , OH A:202binding site for residue OH A 203
04AC4SOFTWAREASN A:15 , TYR A:19 , VAL A:73 , GLU A:74 , HOH A:305 , HOH A:309 , HOH A:339binding site for residue GOL A 204
05AC5SOFTWAREGLN A:99 , ASN A:102 , HIS A:106 , HOH A:303 , GLN C:112binding site for residue GOL A 205
06AC6SOFTWAREGLU B:17 , GLU B:50 , HIS B:53 , GLU B:94 , GLN B:127 , GLU B:130 , OH B:202 , OH B:203 , HOH B:301binding site for residue FEO B 201
07AC7SOFTWAREGLU B:17 , HIS B:53 , TYR B:123 , GLN B:127 , FEO B:201 , OH B:203binding site for residue OH B 202
08AC8SOFTWAREGLU B:17 , GLU B:50 , ILE B:97 , FEO B:201 , OH B:202binding site for residue OH B 203
09AC9SOFTWARESER B:21 , LEU B:22 , GLN B:25 , ALA B:47 , GLN B:48 , HOH B:327 , HOH B:354 , MET E:54 , GLN E:55binding site for residue GOL B 204
10AD1SOFTWARELEU B:2 , ASP B:113 , PRO B:115 , HOH B:392 , HOH B:412 , THR E:98 , ASN E:102binding site for residue GOL B 205
11AD2SOFTWAREGLU C:17 , GLU C:50 , HIS C:53 , FE2 C:202 , OXY C:203 , OH C:204 , HOH C:301binding site for residue FE C 201
12AD3SOFTWAREGLU C:50 , GLU C:94 , GLU C:130 , FE C:201 , OXY C:203 , HOH C:301binding site for residue FE2 C 202
13AD4SOFTWAREGLU C:17 , GLU C:50 , HIS C:53 , GLU C:94 , ILE C:97 , GLN C:127 , GLU C:130 , FE C:201 , FE2 C:202 , OH C:204 , HOH C:301binding site for residue OXY C 203
14AD5SOFTWAREGLU C:17 , HIS C:53 , TYR C:123 , GLN C:127 , FE C:201 , OXY C:203binding site for residue OH C 204
15AD6SOFTWARESER C:21 , LEU C:22 , GLN C:25 , ALA C:47 , GLN C:48 , MET C:51 , HOH C:323 , MET D:51 , MET D:54 , GLN D:55binding site for residue GOL C 205
16AD7SOFTWAREILE C:7 , GLU C:8 , ASN C:11 , LEU C:67binding site for residue GOL C 206
17AD8SOFTWARESER B:136 , ASP B:139 , LYS B:140 , HOH B:314 , THR C:35 , HOH C:306binding site for residue GOL C 207
18AD9SOFTWAREALA C:41 , ARG C:44 , ARG C:45 , HOH C:304 , HOH C:318 , HOH C:328binding site for residue GOL C 208
19AE1SOFTWAREARG C:69 , ASN C:71 , THR C:72 , HOH C:376 , HOH D:371binding site for residue GOL C 209
20AE2SOFTWAREGLU D:17 , GLU D:50 , HIS D:53 , FE D:202 , PER D:203 , OH D:204 , HOH D:301binding site for residue FE D 201
21AE3SOFTWAREGLU D:50 , GLU D:94 , GLU D:130 , FE D:201 , PER D:203binding site for residue FE D 202
22AE4SOFTWAREGLU D:17 , GLU D:50 , HIS D:53 , GLU D:94 , ILE D:97 , GLN D:127 , GLU D:130 , FE D:201 , FE D:202 , OH D:204 , HOH D:301binding site for residue PER D 203
23AE5SOFTWAREGLU D:17 , HIS D:53 , TYR D:123 , GLN D:127 , FE D:201 , PER D:203 , HOH D:301binding site for residue OH D 204
24AE6SOFTWAREGLN D:99 , HIS D:106 , HOH D:375 , GLN E:112binding site for residue GOL D 205
25AE7SOFTWARELYS A:146 , HOH A:308 , GLY D:148 , GLU D:149 , HOH D:362binding site for residue GOL D 206
26AE8SOFTWAREGLU E:17 , GLU E:50 , HIS E:53 , GLU E:94 , GLN E:127 , GLU E:130 , OH E:202 , HOH E:301 , HOH E:303binding site for residue FEO E 201
27AE9SOFTWAREGLU E:17 , HIS E:53 , TYR E:123 , GLN E:127 , FEO E:201 , HOH E:301binding site for residue OH E 202
28AF1SOFTWAREILE E:7 , GLU E:8 , ASN E:11 , LEU E:67 , ARG E:69 , HOH E:306 , HOH E:309 , HOH E:369binding site for residue GOL E 203
29AF2SOFTWAREGLN A:112 , SER B:75 , ARG E:69 , ASN E:71 , THR E:72binding site for residue GOL E 204
30AF3SOFTWAREGLU E:149binding site for residue FE2 E 205
31AF4SOFTWAREGLU F:50 , GLU F:94 , GLU F:130 , FE F:202 , O F:203 , O F:204 , HOH F:301binding site for residue FE F 201
32AF5SOFTWAREGLU F:17 , GLU F:50 , HIS F:53 , FE F:201 , O F:203 , O F:204 , OH F:205 , OH F:206binding site for residue FE F 202
33AF6SOFTWAREGLU F:17 , GLU F:50 , HIS F:53 , GLU F:94 , GLN F:127 , GLU F:130 , FE F:201 , FE F:202 , O F:204 , OH F:205 , OH F:206 , HOH F:301binding site for residue O F 203
34AF7SOFTWAREGLU F:17 , HIS F:53 , TYR F:123 , GLN F:127 , FE F:202 , O F:203 , O F:204 , OH F:206binding site for residue OH F 205
35AF8SOFTWAREGLU F:17 , ALA F:20 , GLU F:50 , ILE F:97 , FE F:202 , O F:203 , OH F:205binding site for residue OH F 206
36AF9SOFTWAREMET A:54 , GLN A:55 , SER F:21 , LEU F:22 , GLN F:25 , ALA F:47 , GLN F:48 , HOH F:346binding site for residue GOL F 207
37AG1SOFTWAREGLU F:94 , ILE F:97 , THR F:98 , TYR F:123 , VAL F:124 , SER F:125 , GLU F:126 , HIS F:128 , GLU F:129 , GLU F:130 , GLU F:131 , FE F:201 , FE F:202 , O F:203 , OH F:205binding site for Di-peptide O F 204 and GLN F 127

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ZTT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZTT)

(-) Sequences/Alignments

Asymmetric 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:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ztt A   2 LKPEMIEKLNEQMNLELYASLLYQQMSAWCSYHTFEGAAAFLRRHAQEEMTHMQRLFDYLTDTGNLPRINTVESPFAEYSSLDELFQETYKHEQLITQKINELAHAAMTNQDYPTFNFLQWYVSEQHEEEKLFKSIIDKLSLAGKSGEGLYFIDKELSTLDT 163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  


Chain B from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ztt B   0 HHLKPEMIEKLNEQMNLELYASLLYQQMSAWCSYHTFEGAAAFLRRHAQEEMTHMQRLFDYLTDTGNLPRINTVESPFAEYSSLDELFQETYKHEQLITQKINELAHAAMTNQDYPTFNFLQWYVSEQHEEEKLFKSIIDKLSLAGKSGEGLYFIDKELSTLDT 163
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159    


Chain C from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ztt C   2 LKPEMIEKLNEQMNLELYASLLYQQMSAWCSYHTFEGAAAFLRRHAQEEMTHMQRLFDYLTDTGNLPRINTVESPFAEYSSLDELFQETYKHEQLITQKINELAHAAMTNQDYPTFNFLQWYVSEQHEEEKLFKSIIDKLSLAGKSGEGLYFIDKELSTLDT 163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  


Chain D from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ztt D   2 LKPEMIEKLNEQMNLELYASLLYQQMSAWCSYHTFEGAAAFLRRHAQEEMTHMQRLFDYLTDTGNLPRINTVESPFAEYSSLDELFQETYKHEQLITQKINELAHAAMTNQDYPTFNFLQWYVSEQHEEEKLFKSIIDKLSLAGKSGEGLYFIDKELSTLDT 163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  


Chain E from PDB  Type:PROTEIN  Length:163
                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ztt E   1 HLKPEMIEKLNEQMNLELYASLLYQQMSAWCSYHTFEGAAAFLRRHAQEEMTHMQRLFDYLTDTGNLPRINTVESPFAEYSSLDELFQETYKHEQLITQKINELAHAAMTNQDYPTFNFLQWYVSEQHEEEKLFKSIIDKLSLAGKSGEGLYFIDKELSTLDT 163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   


Chain F from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ztt F   0 HHLKPEMIEKLNEQMNLELYASLLYQQMSAWCSYHTFEGAAAFLRRHAQEEMTHMQRLFDYLTDTGNLPRINTVESPFAEYSSLDELFQETYKHEQLITQKINELAHAAMTNQDYPTFNFLQWYVSEQHEEEKLFKSIIDKLSLAGKSGEGLYFIDKELSTLDT 163
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
   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 4ZTT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

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        FTNA_ECOLI | P0A998: 1eum 4xgs

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