2YW6 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   STRUCTURAL STUDIES OF N TERMINAL DELETION MUTANT OF DPS FROM MYCOBACTERIUM SMEGMATIS

Authors :   S. Roy, R. Saraswathi, S. Gupta, K. Sekar, D. Chatterji, M. Vijayan

Date :   19 Apr 07 (Deposition) - 17 Jul 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.53

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (4x)

Keywords :   Dna-Binding Protein, Quarternary Assembly, Ferroxidation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Roy, R. Saraswathi, S. Gupta, K. Sekar, D. Chatterji, M. Vijayan
Role Of N And C-Terminal Tails In Dna Binding And Assembly In Dps: Structural Studies Of Mycobacterium Smegmatis Dps Deletion Mutants
J. Mol. Biol. V. 370 752 2007
PubMed-ID: 17543333 | Reference-DOI: 10.1016/J.JMB.2007.05.004

Molecule 1 - DNA PROTECTION DURING STARVATION PROTEIN
	Chains	:	A, B, C
	EC Number	:	1.16.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-MSDPSDELTA9
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	DPS
	Organism Scientific	:	MYCOBACTERIUM SMEGMATIS
	Organism Taxid	:	1772
	Synonym	:	DNA BINDING PROTEIN FROM STATIONARY PHASE CELLS

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (4x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2YW6)

(no "Site" information available for 2YW6)

(no "SS Bond" information available for 2YW6)

(no "Cis Peptide Bond" information available for 2YW6)

(no "SAP(SNP)/Variant" information available for 2YW6)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPS_1	PS00818	Dps protein family signature 1.	DPS_MYCS2	39-55	3	A:39-55 B:39-55 C:39-55
1	DPS_1	PS00818	Dps protein family signature 1.	DPS_MYCSM	39-55	3	A:39-55 B:39-55 C:39-55

Biological Unit 1 (1, 24)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DPS_1	PS00818	Dps protein family signature 1.	DPS_MYCS2	39-55	12	A:39-55 B:39-55 C:39-55
1	DPS_1	PS00818	Dps protein family signature 1.	DPS_MYCSM	39-55	12	A:39-55 B:39-55 C:39-55

(no "Exon" information available for 2YW6)

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:148
 aligned with DPS_MYCS2 | A0R692 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:148
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150        
            DPS_MYCS2    11 DKKASDVADLLQKQLSTYNDLHLTLKHVHWNVVGPNFIGVHEMIDPQVELVRGYADEVAERIATLGKSPKGTPGAIIKDRTWDDYSVERDTVQAHLAALDLVYNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLES 158
               SCOP domains d2yw6a_ A: Dodecameric ferritin homolog                                                                                                              SCOP domains
               CATH domains 2yw6A00 A:11-158  [code=1.20.1260.10, no name defined]                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------DPS_1            ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yw6 A  11 DKKASDVADLLQKQLSTYNDLHLTLKHVHWNVVGPNFIGVHEMIDPQVELVRGYADEVAERIATLGKSPKGTPGAIIKDRTWDDYSVERDTVQAHLAALDLVYNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLES 158
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain A from PDB  Type:PROTEIN  Length:148
 aligned with DPS_MYCSM | P0C558 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:148
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150        
            DPS_MYCSM    11 DKKASDVADLLQKQLSTYNDLHLTLKHVHWNVVGPNFIGVHEMIDPQVELVRGYADEVAERIATLGKSPKGTPGAIIKDRTWDDYSVERDTVQAHLAALDLVYNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLES 158
               SCOP domains d2yw6a_ A: Dodecameric ferritin homolog                                                                                                              SCOP domains
               CATH domains 2yw6A00 A:11-158  [code=1.20.1260.10, no name defined]                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------DPS_1            ------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yw6 A  11 DKKASDVADLLQKQLSTYNDLHLTLKHVHWNVVGPNFIGVHEMIDPQVELVRGYADEVAERIATLGKSPKGTPGAIIKDRTWDDYSVERDTVQAHLAALDLVYNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLES 158
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:150
 aligned with DPS_MYCS2 | A0R692 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:150
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
            DPS_MYCS2    11 DKKASDVADLLQKQLSTYNDLHLTLKHVHWNVVGPNFIGVHEMIDPQVELVRGYADEVAERIATLGKSPKGTPGAIIKDRTWDDYSVERDTVQAHLAALDLVYNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLESAG 160
               SCOP domains d2yw6b_ B: Dodecameric ferritin homolog                                                                                                                SCOP domains
               CATH domains 2yw6B00 B:11-160  [code=1.20.1260.10, no name defined]                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------DPS_1            --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yw6 B  11 DKKASDVADLLQKQLSTYNDLHLTLKHVHWNVVGPNFIGVHEMIDPQVELVRGYADEVAERIATLGKSPKGTPGAIIKDRTWDDYSVERDTVQAHLAALDLVYNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLESAG 160
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:150
 aligned with DPS_MYCSM | P0C558 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:150
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
            DPS_MYCSM    11 DKKASDVADLLQKQLSTYNDLHLTLKHVHWNVVGPNFIGVHEMIDPQVELVRGYADEVAERIATLGKSPKGTPGAIIKDRTWDDYSVERDTVQAHLAALDLVYNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLESAG 160
               SCOP domains d2yw6b_ B: Dodecameric ferritin homolog                                                                                                                SCOP domains
               CATH domains 2yw6B00 B:11-160  [code=1.20.1260.10, no name defined]                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ----------------------------DPS_1            --------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yw6 B  11 DKKASDVADLLQKQLSTYNDLHLTLKHVHWNVVGPNFIGVHEMIDPQVELVRGYADEVAERIATLGKSPKGTPGAIIKDRTWDDYSVERDTVQAHLAALDLVYNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLESAG 160
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain C from PDB  Type:PROTEIN  Length:150
 aligned with DPS_MYCS2 | A0R692 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:150
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
            DPS_MYCS2    11 DKKASDVADLLQKQLSTYNDLHLTLKHVHWNVVGPNFIGVHEMIDPQVELVRGYADEVAERIATLGKSPKGTPGAIIKDRTWDDYSVERDTVQAHLAALDLVYNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLESAG 160
               SCOP domains d2yw6c_ C: Dodecameric ferritin homolog                                                                                                                SCOP domains
               CATH domains 2yw6C00 C:11-160  [code=1.20.1260.10, no name defined]                                                                                                 CATH domains
           Pfam domains (1) -------Ferritin-2yw6C01 C:18-160                                                                                                                       Pfam domains (1)
           Pfam domains (2) -------Ferritin-2yw6C02 C:18-160                                                                                                                       Pfam domains (2)
           Pfam domains (3) -------Ferritin-2yw6C03 C:18-160                                                                                                                       Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------DPS_1            --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yw6 C  11 DKKASDVADLLQKQLSTYNDLHLTLKHVHWNVVGPNFIGVHEMIDPQVELVRGYADEVAERIATLGKSPKGTPGAIIKDRTWDDYSVERDTVQAHLAALDLVYNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLESAG 160
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain C from PDB  Type:PROTEIN  Length:150
 aligned with DPS_MYCSM | P0C558 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:150
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
            DPS_MYCSM    11 DKKASDVADLLQKQLSTYNDLHLTLKHVHWNVVGPNFIGVHEMIDPQVELVRGYADEVAERIATLGKSPKGTPGAIIKDRTWDDYSVERDTVQAHLAALDLVYNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLESAG 160
               SCOP domains d2yw6c_ C: Dodecameric ferritin homolog                                                                                                                SCOP domains
               CATH domains 2yw6C00 C:11-160  [code=1.20.1260.10, no name defined]                                                                                                 CATH domains
           Pfam domains (1) -------Ferritin-2yw6C01 C:18-160                                                                                                                       Pfam domains (1)
           Pfam domains (2) -------Ferritin-2yw6C02 C:18-160                                                                                                                       Pfam domains (2)
           Pfam domains (3) -------Ferritin-2yw6C03 C:18-160                                                                                                                       Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ----------------------------DPS_1            --------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yw6 C  11 DKKASDVADLLQKQLSTYNDLHLTLKHVHWNVVGPNFIGVHEMIDPQVELVRGYADEVAERIATLGKSPKGTPGAIIKDRTWDDYSVERDTVQAHLAALDLVYNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLESAG 160
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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: Dodecameric ferritin homolog (44)

Mycobacterium smegmatis [TaxId: 1772] (5)

1a	d2yw6a_	A:
1b	d2yw6b_	B:
1c	d2yw6c_	C:

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)

Mycobacterium smegmatis. Organism_taxid: 1772. (1)

1a	2yw6B00	B:11-160
1b	2yw6C00	C:11-160
1c	2yw6A00	A:11-158

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Ferritin (83)

Mycobacterium smegmatis (6)

1a	Ferritin-2yw6C01	C:18-160
1b	Ferritin-2yw6C02	C:18-160
1c	Ferritin-2yw6C03	C:18-160

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (DPS_MYCSM | P0C558)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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.
	GO:0009295	nucleoid	The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.

Chain A,B,C (DPS_MYCS2 | A0R692)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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.
	GO:0009295	nucleoid	The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.

Asymmetric Unit
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	Cis Peptide Bonds
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Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2yw6
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	DPS_MYCSM \| P0C558
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	1.16.-.-
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UniProtKB/Swiss-Prot
	DPS_MYCS2 \| A0R692	:	1uvh 1vei 1vel 1veq 2yw7
	DPS_MYCSM \| P0C558	:	1uvh 1vei 1vel 1veq 2yw7

(no "Related Entries Specified in the PDB File" available for 2YW6)

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