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(-) Description

Title :  MYCOBACTERIUM SMEGMATIS DPS
 
Authors :  S. Roy, S. Gupta, S. Das, K. Sekar, D. Chatterji, M. Vijayan
Date :  31 Mar 04  (Deposition) - 29 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Dna-Binding Protein, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Roy, S. Gupta, S. Das, K. Sekar, D. Chatterji, M. Vijayan
X-Ray Analysis Of Mycobacterium Smegmatis Dps And A Comparative Study Involving Other Dps And Dps-Like Molecule
J. Mol. Biol. V. 339 1103 2004
PubMed-ID: 15178251  |  Reference-DOI: 10.1016/J.JMB.2004.04.042

(-) Compounds

Molecule 1 - STARVATION-INDUCED DNA PROTECTING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-DPS, PGEM-T EASY
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 1772
    Synonym: DPS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (12x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2SO412Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:39 , ASP A:66 , GLU A:70BINDING SITE FOR RESIDUE FE A 184
2AC2SOFTWARELYS A:36 , ASP A:66 , HOH A:213BINDING SITE FOR RESIDUE FE A 185
3AC3SOFTWARELYS A:77 , SER A:78 , LYS A:80 , ARG A:99BINDING SITE FOR RESIDUE SO4 A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VEI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VEI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VEI)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DPS_1PS00818 Dps protein family signature 1.DPS_MYCS239-55  1A:39-55
DPS_MYCSM39-55  1A:39-55
Biological Unit 1 (1, 24)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DPS_1PS00818 Dps protein family signature 1.DPS_MYCS239-55  12A:39-55
DPS_MYCSM39-55  12A:39-55

(-) Exons   (0, 0)

(no "Exon" information available for 1VEI)

(-) 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:175
 aligned with DPS_MYCS2 | A0R692 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     
            DPS_MYCS2     1 MTSFTIPGLSDKKASDVADLLQKQLSTYNDLHLTLKHVHWNVVGPNFIGVHEMIDPQVELVRGYADEVAERIATLGKSPKGTPGAIIKDRTWDDYSVERDTVQAHLAALDLVYNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLESAGGQLTHEGQSTEKGAA 175
               SCOP domains d1veia_ A: Dodecameric ferritin homolog                                                                                                                                         SCOP domains
               CATH domains 1veiA00 A:1-175  [code=1.20.1260.10, no name defined]                                                                                                                           CATH domains
               Pfam domains -----------------Ferritin-1veiA01 A:18-160                                                                                                                      --------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------DPS_1            ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vei A   1 MTSFTIPGLSDKKASDVADLLQKQLSTYNDLHLTLKHVHWNVVGPNFIGVHEMIDPQVELVRGYADEVAERIATLGKSPKGTPGAIIKDRTWDDYSVERDTVQAHLAALDLVYNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLESAGGQLTHEGQSTEKGAA 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     


Chain A from PDB  Type:PROTEIN  Length:175
 aligned with DPS_MYCSM | P0C558 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     
            DPS_MYCSM     1 MTSFTIPGLSDKKASDVADLLQKQLSTYNDLHLTLKHVHWNVVGPNFIGVHEMIDPQVELVRGYADEVAERIATLGKSPKGTPGAIIKDRTWDDYSVERDTVQAHLAALDLVYNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLESAGGQLTHEGQSTEKGAA 175
               SCOP domains d1veia_ A: Dodecameric ferritin homolog                                                                                                                                         SCOP domains
               CATH domains 1veiA00 A:1-175  [code=1.20.1260.10, no name defined]                                                                                                                           CATH domains
               Pfam domains -----------------Ferritin-1veiA01 A:18-160                                                                                                                      --------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------DPS_1            ------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vei A   1 MTSFTIPGLSDKKASDVADLLQKQLSTYNDLHLTLKHVHWNVVGPNFIGVHEMIDPQVELVRGYADEVAERIATLGKSPKGTPGAIIKDRTWDDYSVERDTVQAHLAALDLVYNGVIEDTRKSIEKLEDLDLVSQDLLIAHAGELEKFQWFVRAHLESAGGQLTHEGQSTEKGAA 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Ferritin (185)

(-) Gene Ontology  (10, 20)

Asymmetric Unit(hide GO term definitions)
Chain A   (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.

Chain A   (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.

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1vel MYCOBACTERIUM SMEGMATIS DPS, TETRAGONAL FORM, (P 43 21 2)
1veq MYCOBACTERIUM SMEGMATIS DPS, HEXAGONAL FORM, (P63)