2BK6 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Title :   THE X-RAY CRYSTAL STRUCTURE OF THE LISTERIA INNOCUA H31G DPS MUTANT.

Authors :   A. Ilari, M. C. Latella, F. Ribacchi, M. Su, L. Giangiacomo, S. Stefanini, N. D. Chasteen, E. Chiancone

Date :   11 Feb 05 (Deposition) - 14 Feb 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.19

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F  (2x)

Keywords :   Dps (Dna Binding Protein From Starved Cells), Ferroxidase Center, Mutagenesis Study, Iron Oxidation And Storage, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Ilari, M. C. Latella, P. Ceci, F. Ribacchi, M. Su, L. Giangiacomo, S. Stefanini, N. D. Chasteen, E. Chiancone
The Unusual Intersubunit Ferroxidase Center Of Listeria Innocua Dps Is Required For Hydrogen Peroxide Detoxification But Not For Iron Uptake. A Study With Site-Specific Mutants
Biochemistry V. 44 5579 2005
PubMed-ID: 15823016 | Reference-DOI: 10.1021/BI050005E
(for further references see the PDB file header)

Molecule 1 - NON-HEME IRON-CONTAINING FERRITIN
	Chains	:	A, B, C, D, E, F,
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	DE3
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Mutation	:	YES
	Organism Scientific	:	LISTERIA INNOCUA
	Organism Taxid	:	1642
	Other Details	:	H31G MUTANT OF DPS FROM LISTERIA INNOCUA

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (2x)	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2BK6)

(no "Site" information available for 2BK6)

(no "SS Bond" information available for 2BK6)

(no "Cis Peptide Bond" information available for 2BK6)

(no "SAP(SNP)/Variant" information available for 2BK6)

Asymmetric Unit (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPS_1	PS00818	Dps protein family signature 1.	DPS_LISIN	31-47	6	A:32-47 B:32-47 C:32-47 D:32-47 E:32-47 F:32-47
2	DPS_2	PS00819	Dps protein family signature 2.	DPS_LISIN	57-71	6	A:57-71 B:57-71 C:57-71 D:57-71 E:57-71 F:57-71

Biological Unit 1 (2, 24)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPS_1	PS00818	Dps protein family signature 1.	DPS_LISIN	31-47	12	A:32-47 B:32-47 C:32-47 D:32-47 E:32-47 F:32-47
2	DPS_2	PS00819	Dps protein family signature 2.	DPS_LISIN	57-71	12	A:57-71 B:57-71 C:57-71 D:57-71 E:57-71 F:57-71

(no "Exon" information available for 2BK6)

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:150
 aligned with DPS_LISIN | P80725 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:150
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156
            DPS_LISIN     7 VDTKEFLNHQVANLNVFTVKIHQIHWYMRGHNFFTLHEKMDDLYSEFGEQMDEVAERLLAIGGSPFSTLKEFLENASVEEAPYTKPKTMDQLMEDLVGTLELLRDEYKQGIELTDKEGDDVTNDMLIAFKASIDKHIWMFKAFLGKAPLE 156
               SCOP domains d2bk6a1 A:7-156 Dodecameric ferritin homolog                                                                                                           SCOP domains
               CATH domains 2bk6A00 A:7-156  [code=1.20.1260.10, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------DPS_1            ---------DPS_2          ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bk6 A   7 VDTKEFLNHQVANLNVFTVKIHQIGWYMRGHNFFTLHEKMDDLYSEFGEQMDEVAERLLAIGGSPFSTLKEFLENASVEEAPYTKPKTMDQLMEDLVGTLELLRDEYKQGIELTDKEGDDVTNDMLIAFKASIDKHIWMFKAFLGKAPLE 156
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156

Chain B from PDB  Type:PROTEIN  Length:150
 aligned with DPS_LISIN | P80725 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:150
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156
            DPS_LISIN     7 VDTKEFLNHQVANLNVFTVKIHQIHWYMRGHNFFTLHEKMDDLYSEFGEQMDEVAERLLAIGGSPFSTLKEFLENASVEEAPYTKPKTMDQLMEDLVGTLELLRDEYKQGIELTDKEGDDVTNDMLIAFKASIDKHIWMFKAFLGKAPLE 156
               SCOP domains d2bk6b_ B: automated matches                                                                                                                           SCOP domains
               CATH domains 2bk6B00 B:7-156  [code=1.20.1260.10, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------DPS_1            ---------DPS_2          ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bk6 B   7 VDTKEFLNHQVANLNVFTVKIHQIGWYMRGHNFFTLHEKMDDLYSEFGEQMDEVAERLLAIGGSPFSTLKEFLENASVEEAPYTKPKTMDQLMEDLVGTLELLRDEYKQGIELTDKEGDDVTNDMLIAFKASIDKHIWMFKAFLGKAPLE 156
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156

Chain C from PDB  Type:PROTEIN  Length:154
 aligned with DPS_LISIN | P80725 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:154
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152    
            DPS_LISIN     3 TINSVDTKEFLNHQVANLNVFTVKIHQIHWYMRGHNFFTLHEKMDDLYSEFGEQMDEVAERLLAIGGSPFSTLKEFLENASVEEAPYTKPKTMDQLMEDLVGTLELLRDEYKQGIELTDKEGDDVTNDMLIAFKASIDKHIWMFKAFLGKAPLE 156
               SCOP domains d2bk6c_ C: automated matches                                                                                                                               SCOP domains
               CATH domains 2bk6C00 C:3-156  [code=1.20.1260.10, no name defined]                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------DPS_1            ---------DPS_2          ------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bk6 C   3 TINSVDTKEFLNHQVANLNVFTVKIHQIGWYMRGHNFFTLHEKMDDLYSEFGEQMDEVAERLLAIGGSPFSTLKEFLENASVEEAPYTKPKTMDQLMEDLVGTLELLRDEYKQGIELTDKEGDDVTNDMLIAFKASIDKHIWMFKAFLGKAPLE 156
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain D from PDB  Type:PROTEIN  Length:150
 aligned with DPS_LISIN | P80725 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:150
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156
            DPS_LISIN     7 VDTKEFLNHQVANLNVFTVKIHQIHWYMRGHNFFTLHEKMDDLYSEFGEQMDEVAERLLAIGGSPFSTLKEFLENASVEEAPYTKPKTMDQLMEDLVGTLELLRDEYKQGIELTDKEGDDVTNDMLIAFKASIDKHIWMFKAFLGKAPLE 156
               SCOP domains d2bk6d_ D: automated matches                                                                                                                           SCOP domains
               CATH domains 2bk6D00 D:7-156  [code=1.20.1260.10, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------DPS_1            ---------DPS_2          ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bk6 D   7 VDTKEFLNHQVANLNVFTVKIHQIGWYMRGHNFFTLHEKMDDLYSEFGEQMDEVAERLLAIGGSPFSTLKEFLENASVEEAPYTKPKTMDQLMEDLVGTLELLRDEYKQGIELTDKEGDDVTNDMLIAFKASIDKHIWMFKAFLGKAPLE 156
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156

Chain E from PDB  Type:PROTEIN  Length:150
 aligned with DPS_LISIN | P80725 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:150
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156
            DPS_LISIN     7 VDTKEFLNHQVANLNVFTVKIHQIHWYMRGHNFFTLHEKMDDLYSEFGEQMDEVAERLLAIGGSPFSTLKEFLENASVEEAPYTKPKTMDQLMEDLVGTLELLRDEYKQGIELTDKEGDDVTNDMLIAFKASIDKHIWMFKAFLGKAPLE 156
               SCOP domains d2bk6e_ E: automated matches                                                                                                                           SCOP domains
               CATH domains 2bk6E00 E:7-156  [code=1.20.1260.10, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------DPS_1            ---------DPS_2          ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bk6 E   7 VDTKEFLNHQVANLNVFTVKIHQIGWYMRGHNFFTLHEKMDDLYSEFGEQMDEVAERLLAIGGSPFSTLKEFLENASVEEAPYTKPKTMDQLMEDLVGTLELLRDEYKQGIELTDKEGDDVTNDMLIAFKASIDKHIWMFKAFLGKAPLE 156
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156

Chain F from PDB  Type:PROTEIN  Length:150
 aligned with DPS_LISIN | P80725 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:150
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156
            DPS_LISIN     7 VDTKEFLNHQVANLNVFTVKIHQIHWYMRGHNFFTLHEKMDDLYSEFGEQMDEVAERLLAIGGSPFSTLKEFLENASVEEAPYTKPKTMDQLMEDLVGTLELLRDEYKQGIELTDKEGDDVTNDMLIAFKASIDKHIWMFKAFLGKAPLE 156
               SCOP domains d2bk6f_ F: automated matches                                                                                                                           SCOP domains
               CATH domains 2bk6F00 F:7-156  [code=1.20.1260.10, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------DPS_1            ---------DPS_2          ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bk6 F   7 VDTKEFLNHQVANLNVFTVKIHQIGWYMRGHNFFTLHEKMDDLYSEFGEQMDEVAERLLAIGGSPFSTLKEFLENASVEEAPYTKPKTMDQLMEDLVGTLELLRDEYKQGIELTDKEGDDVTNDMLIAFKASIDKHIWMFKAFLGKAPLE 156
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Ferritin-like (533)

Superfamily: Ferritin-like (489)

Family: Ferritin (232)

Protein domain: automated matches (70)

Listeria innocua [TaxId: 1642] (3)

1a	d2bk6b_	B:
1b	d2bk6c_	C:
1c	d2bk6d_	D:
1d	d2bk6e_	E:
1e	d2bk6f_	F:

Protein domain: Dodecameric ferritin homolog (44)

Listeria innocua [TaxId: 1642] (4)

d2bk6a1

A:7-156

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Ferritin; (180)

Homologous Superfamily: [code=1.20.1260.10, no name defined] (180)

Listeria innocua. Organism_taxid: 1642. (3)

1a	2bk6C00	C:3-156
1b	2bk6A00	A:7-156
1c	2bk6B00	B:7-156
1d	2bk6D00	D:7-156
1e	2bk6E00	E:7-156
1f	2bk6F00	F:7-156

(no "Pfam Domain" information available for 2BK6)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (DPS_LISIN | P80725)

molecular function
	GO:0008199	ferric iron binding	Interacting selectively and non-covalently with ferric iron, Fe(III).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016722	oxidoreductase activity, oxidizing metal ions	Catalysis of an oxidation-reduction in which the oxidation state of metal ion is altered.
biological process
	GO:0006879	cellular iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006950	response to stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2bk6)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2bk6
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UniProtKB/Swiss-Prot
	DPS_LISIN \| P80725	:	1qgh 2bjy 2bkc

1qgh	THE X-RAY STRUCTURE OF THE UNUSUAL DODECAMERIC FERRITIN FROM LISTERIA INNOCUA, REVEALS A NOVEL INTERSUBUNIT IRON BINDING SITE.
2bjy	THE X-RAY CRYSTAL STRUCTURE OF LISTERIA INNOCUA DPS H31G-H43G MUTANT.

Description

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Ligands, Modified Residues, Ions (0, 0)

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SCOP Domains (2, 6)

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