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(-) Description

Title :  CRYSTAL STRUCTURE OF OSMC FROM E. COLI
 
Authors :  D. H. Shin, I. -G. Choi, D. Busso, J. Jancarik, H. Yokota, R. Kim, S. - H. Kim, Berkeley Structural Genomics Center (Bsgc)
Date :  12 Feb 03  (Deposition) - 02 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)
Biol. Unit 5:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)
Biol. Unit 6:  A,B,C,D,E,F  (1x)
Keywords :  Crystal Structure, Osmc, Structural Genomics, Peroxiredoxin, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Shin, I. G. Choi, D. Busso, J. Jancarik, H. Yokota, R. Kim, S. H. Kim
Structure Of Osmc From Escherichia Coli: A Salt-Shock-Induced Protein.
Acta Crystallogr. , Sect. D V. 60 903 2004
PubMed-ID: 15103136  |  Reference-DOI: 10.1107/S0907444904005013
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OSMOTICALLY INDUCIBLE PROTEIN C
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSKB3
    Expression System Strain: B834(DE3)/PSJS1244
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: OSMC OR B1482
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF
Biological Unit 4 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)
Biological Unit 5 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)
Biological Unit 6 (1x): ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1NYE)

(-) Sites  (0, 0)

(no "Site" information available for 1NYE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NYE)

(-) Exons   (0, 0)

(no "Exon" information available for 1NYE)

(-) 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:143
 aligned with OSMC_ECOLI | P0C0L2 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   
          OSMC_ECOLI      1 MTIHKKGQAHWEGDIKRGKGTVSTESGVLNQQPYGFNTRFEGEKGTNPEELIGAAHAACFSMALSLMLGEAGFTPTSIDTTADVSLDKVDAGFAITKIALKSEVAVPGIDASTFDGIIQKAKAGCPVSQVLKAEITLDYQLKS  143
               SCOP domains d1nyea_ A: Osmotically inducible protein OsmC                                                                                                   SCOP domains
               CATH domains 1nyeA00 A:21-163  [code=3.30.300.20, no name defined]                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee......eeeeee.......eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeeee..eeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nye A   21 MTIHKKGQAHWEGDIKRGKGTVSTESGVLNQQPYGFNTRFEGEKGTNPEELIGAAHAACFSMALSLMLGEAGFTPTSIDTTADVSLDKVDAGFAITKIALKSEVAVPGIDASTFDGIIQKAKAGCPVSQVLKAEITLDYQLKS  163
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160   


Chain B from PDB  Type:PROTEIN  Length:143
 aligned with OSMC_ECOLI | P0C0L2 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   
          OSMC_ECOLI      1 MTIHKKGQAHWEGDIKRGKGTVSTESGVLNQQPYGFNTRFEGEKGTNPEELIGAAHAACFSMALSLMLGEAGFTPTSIDTTADVSLDKVDAGFAITKIALKSEVAVPGIDASTFDGIIQKAKAGCPVSQVLKAEITLDYQLKS  143
               SCOP domains d1nyeb_ B: Osmotically inducible protein OsmC                                                                                                   SCOP domains
               CATH domains 1nyeB00 B:221-363  [code=3.30.300.20, no name defined]                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee......eeeeee.......eeehhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeee..eeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nye B  221 MTIHKKGQAHWEGDIKRGKGTVSTESGVLNQQPYGFNTRFEGEKGTNPEELIGAAHAACFSMALSLMLGEAGFTPTSIDTTADVSLDKVDAGFAITKIALKSEVAVPGIDASTFDGIIQKAKAGCPVSQVLKAEITLDYQLKS  363
                                   230       240       250       260       270       280       290       300       310       320       330       340       350       360   


Chain C from PDB  Type:PROTEIN  Length:153
 aligned with OSMC_ECOLI | P0C0L2 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:153
                                      1                                                                                                                                              
                                     -|       10        20        30        40        50        60        70        80        90       100       110       120       130       140   
          OSMC_ECOLI      - ----------MTIHKKGQAHWEGDIKRGKGTVSTESGVLNQQPYGFNTRFEGEKGTNPEELIGAAHAACFSMALSLMLGEAGFTPTSIDTTADVSLDKVDAGFAITKIALKSEVAVPGIDASTFDGIIQKAKAGCPVSQVLKAEITLDYQLKS  143
               SCOP domains d1nyec_ C: Osmotically inducible protein OsmC                                                                                                             SCOP domains
               CATH domains 1nyeC00 C:411-563  [code=3.30.300.20, no name defined]                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeee......eeeeee.......eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeeee..eeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nye C  411 TTENLYFQGHMTIHKKGQAHWEGDIKRGKGTVSTESGVLNQQPYGFNTRFEGEKGTNPEELIGAAHAACFSMALSLMLGEAGFTPTSIDTTADVSLDKVDAGFAITKIALKSEVAVPGIDASTFDGIIQKAKAGCPVSQVLKAEITLDYQLKS  563
                                   420       430       440       450       460       470       480       490       500       510       520       530       540       550       560   


Chain D from PDB  Type:PROTEIN  Length:162
 aligned with OSMC_ECOLI | P0C0L2 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:162
                                               1                                                                                                                                              
                                     -         1        11        21        31        41        51        61        71        81        91       101       111       121       131       141  
          OSMC_ECOLI      - -------------------MTIHKKGQAHWEGDIKRGKGTVSTESGVLNQQPYGFNTRFEGEKGTNPEELIGAAHAACFSMALSLMLGEAGFTPTSIDTTADVSLDKVDAGFAITKIALKSEVAVPGIDASTFDGIIQKAKAGCPVSQVLKAEITLDYQLKS  143
               SCOP domains d1nyed_ D: Osmotically inducible protein OsmC                                                                                                                      SCOP domains
               CATH domains 1nyeD00 D:602-763  [code=3.30.300.20, no name defined]                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee................eeeeeeeeee......eeeeee.......eeehhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeee......eeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1nye D  602 HHHHDYDIPTTENLYFQGHMTIHKKGQAHWEGDIKRGKGTVSTESGVLNQQPYGFNTRFEGEKGTNPEELIGAAHAACFSMALSLMLGEAGFTPTSIDTTADVSLDKVDAGFAITKIALKSEVAVPGIDASTFDGIIQKAKAGCPVSQVLKAEITLDYQLKS  763
                                   611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761  


Chain E from PDB  Type:PROTEIN  Length:151
 aligned with OSMC_ECOLI | P0C0L2 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:151
                                    1                                                                                                                                              
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142 
          OSMC_ECOLI      - --------MTIHKKGQAHWEGDIKRGKGTVSTESGVLNQQPYGFNTRFEGEKGTNPEELIGAAHAACFSMALSLMLGEAGFTPTSIDTTADVSLDKVDAGFAITKIALKSEVAVPGIDASTFDGIIQKAKAGCPVSQVLKAEITLDYQLKS  143
               SCOP domains d1nyee_ E: Osmotically inducible protein OsmC                                                                                                           SCOP domains
               CATH domains 1nyeE00 E:813-963  [code=3.30.300.20, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.eeeeeeeeee......eeeeee.......ee.............hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeee..eeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nye E  813 ENLYFQGHMTIHKKGQAHWEGDIKRGKGTVSTESGVLNQQPYGFNTRFEGEKGTNPEELIGAAHAACFSMALSLMLGEAGFTPTSIDTTADVSLDKVDAGFAITKIALKSEVAVPGIDASTFDGIIQKAKAGCPVSQVLKAEITLDYQLKS  963
                                   822       832       842       852       862       872       882       892       902       912       922       932       942       952       962 


Chain F from PDB  Type:PROTEIN  Length:158
 aligned with OSMC_ECOLI | P0C0L2 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:162
                                               1                                                                                                                                              
                                     -         1        11        21        31        41        51        61        71        81        91       101       111       121       131       141  
          OSMC_ECOLI      - -------------------MTIHKKGQAHWEGDIKRGKGTVSTESGVLNQQPYGFNTRFEGEKGTNPEELIGAAHAACFSMALSLMLGEAGFTPTSIDTTADVSLDKVDAGFAITKIALKSEVAVPGIDASTFDGIIQKAKAGCPVSQVLKAEITLDYQLKS  143
               SCOP domains d1nyef_ F: Osmotically inducible protein OsmC                                                                                                                      SCOP domains
               CATH domains 1nyeF00 F:1002-1163  [code=3.30.300.20, no name defined]                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..........hhhh.eeeeeeeeeee......eeeeee.......eee.....----...hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeee..eeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1nye F 1002 HHHHDYDIPTTENLYFQGHMTIHKKGQAHWEGDIKRGKGTVSTESGVLNQQPYGFNTR----KGTNPEELIGAAHAACFSMALSLMLGEAGFTPTSIDTTADVSLDKVDAGFAITKIALKSEVAVPGIDASTFDGIIQKAKAGCPVSQVLKAEITLDYQLKS 1163
                                  1011      1021      1031      1041      1051       | -  |   1071      1081      1091      1101      1111      1121      1131      1141      1151      1161  
                                                                                  1059 1064
   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  (1, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1NYE)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (OSMC_ECOLI | P0C0L2)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    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:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
    GO:0051920    peroxiredoxin activity    Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0006972    hyperosmotic response    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 detection of, or exposure to, a hyperosmotic environment, i.e. an environment with a higher concentration of solutes than the organism or 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:0033194    response to hydroperoxide    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 hydroperoxide stimulus. Hydroperoxides are monosubstitution products of hydrogen peroxide, HOOH.
    GO:0006979    response to oxidative 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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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