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(-) Description

Title :  STRUCTURE OF E. COLI MONOTHIOL GLUTAREDOXIN GRX4 HOMODIMER
 
Authors :  T. Iwema, A. Picchiocci, D. A. K. Traore, J. -L. Ferrer, F. Chauvat, L. J
Date :  12 Mar 09  (Deposition) - 23 Jun 09  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Redox-Active Center, Iron-Sulfur Cluster Scaffolder, Fe2S2, Homodimer, Transport, Glutathione, Thioredoxin Fold, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Iwema, A. Picciocchi, D. A. K. Traore, J. -L. Ferrer, F. Chauvat, L. Jacquamet
Structural Basis For Delivery Of The Intact [Fe2S2] Cluster By Monothiol Glutaredoxin.
Biochemistry V. 48 6041 2009
PubMed-ID: 19505088  |  Reference-DOI: 10.1021/BI900440M

(-) Compounds

Molecule 1 - GLUTAREDOXIN-4
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: GLUTATHIONE, FE2S2 CLUSTER
    Synonym: GRX4, MONOTHIOL GLUTAREDOXIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB
Biological Unit 2 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2GSH2Ligand/IonGLUTATHIONE
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2GSH4Ligand/IonGLUTATHIONE
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2GSH2Ligand/IonGLUTATHIONE
3NA-1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:22 , CYS A:30 , GSH A:1115 , LYS B:22 , CYS B:30 , GSH B:1115BINDING SITE FOR RESIDUE FES A1114
2AC2SOFTWARELYS A:22 , CYS A:30 , PHE A:32 , ARG A:59 , THR A:70 , PHE A:71 , GLY A:83 , CYS A:84 , ASP A:85 , FES A:1114 , HOH A:2075 , HOH A:2089 , HOH A:2090 , HOH A:2092 , HOH A:2094 , HOH A:2096 , HOH A:2097 , ASP B:85 , HOH B:2027BINDING SITE FOR RESIDUE GSH A1115
3AC3SOFTWAREPRO A:28 , CYS A:30 , GLY A:31 , HOH A:2009 , HOH A:2012 , ARG B:59BINDING SITE FOR RESIDUE NA A1116
4AC4SOFTWARETHR A:70 , FES A:1114 , HOH A:2094 , LYS B:22 , CYS B:30 , PHE B:32 , ARG B:59 , THR B:70 , PHE B:71 , GLY B:83 , CYS B:84 , ASP B:85 , HOH B:2062 , HOH B:2066 , HOH B:2081 , HOH B:2082 , HOH B:2083 , HOH B:2084 , HOH B:2085BINDING SITE FOR RESIDUE GSH B1115

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:71 -Pro A:72
2Phe B:71 -Pro B:72

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTAREDOXIN_2PS51354 Glutaredoxin domain profile.GLRX4_ECOLI5-107
 		  2A:5-107
B:5-107
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTAREDOXIN_2PS51354 Glutaredoxin domain profile.GLRX4_ECOLI5-107
 		  4A:5-107
B:5-107
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTAREDOXIN_2PS51354 Glutaredoxin domain profile.GLRX4_ECOLI5-107
 		  2A:5-107
B:5-107

(-) Exons   (0, 0)

(no "Exon" information available for 2WCI)

(-) 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:113
 aligned with GLRX4_ECOLI | P0AC69 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:113
                                    10        20        30        40        50        60        70        80        90       100       110   
          GLRX4_ECOLI     1 MSTTIEKIQRQIAENPILLYMKGSPKLPSCGFSAQAVQALAACGERFAYVDILQNPDIRAELPKYANWPTFPQLWVDGELVGGCDIVIEMYQRGELQQLIKETAAKYKSEEPD 113
               SCOP domains d2wcia_ A: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----GLUTAREDOXIN_2  PDB: A:5-107 UniProt: 5-107                                                            ------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2wci A   1 MSTTIEKIQRQIAENPILLYMKGSPKLPSCGFSAQAVQALAACGERFAYVDILQNPDIRAELPKYANWPTFPQLWVDGELVGGCDIVIEMYQRGELQQLIKETAAKYKSEEPD 113
                                    10        20        30        40        50        60        70        80        90       100       110   


Chain B from PDB  Type:PROTEIN  Length:112
 aligned with GLRX4_ECOLI | P0AC69 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:112
                                    12        22        32        42        52        62        72        82        92       102       112  
          GLRX4_ECOLI     3 TTIEKIQRQIAENPILLYMKGSPKLPSCGFSAQAVQALAACGERFAYVDILQNPDIRAELPKYANWPTFPQLWVDGELVGGCDIVIEMYQRGELQQLIKETAAKYKSEEPDA 114
               SCOP domains d2wcib_ B: automated matches                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------Glutaredoxin-2wciB01 B:17-81                                     --------------------------------- Pfam domains (1)
           Pfam domains (2) --------------Glutaredoxin-2wciB02 B:17-81                                     --------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GLUTAREDOXIN_2  PDB: B:5-107 UniProt: 5-107                                                            ------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2wci B   3 TTIEKIQRQIAENPILLYMKGSPKLPSCGFSAQAVQALAACGERFAYVDILQNPDIRAELPKYANWPTFPQLWVDGELVGGCDIVIEMYQRGELQQLIKETAAKYKSEEPDA 114
                                    12        22        32        42        52        62        72        82        92       102       112
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WCI)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GLRX4_ECOLI | P0AC69)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within 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.
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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 Related Entries

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UniProtKB/Swiss-Prot
        GLRX4_ECOLI | P0AC69: 1yka

(-) Related Entries Specified in the PDB File

1yka SOLUTION STRUCTURE OF GRX4, A MONOTHIOL GLUTAREDOXIN FROM E. COLI.