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(-) Description

Title :  GLUTAREDOXIN-1-RIBONUCLEOTIDE REDUCTASE B1 MIXED DISULFIDE BOND
 
Authors :  M. J. Berardi, J. H. Bushweller
Date :  12 Apr 99  (Deposition) - 01 Jan 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Glutaredoxin, Ribonucleotide Reductase, Disulfide, Electron Transfer, Electron Transport/Oxidoreductase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. J. Berardi, J. H. Bushweller
Binding Specificity And Mechanistic Insight Into Glutaredoxin-Catalyzed Protein Disulfide Reduction.
J. Mol. Biol. V. 292 151 1999
PubMed-ID: 10493864  |  Reference-DOI: 10.1006/JMBI.1999.3067
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (GLUTAREDOXIN 1)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsINTERMOLECULAR DISULFIDE BRIDGE BETWEEN;
CYS 11 A AND CYS 148 B
    SynonymGRX 1
 
Molecule 2 - PROTEIN (RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1)
    ChainsB
    EC Number1.17.4.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentAPHA CHAIN, B1 SUBUNIT
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsINTERMOLECULAR DISULFIDE BRIDGE CYS759
    SynonymRIBONUCLEOTIDE REDUCTASE, B1 PROTEIN, R1 PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1QFN)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:11 -B:148

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Val A:59 -Pro A:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTAREDOXIN_2PS51354 Glutaredoxin domain profile.GLRX1_ECOLI1-85  1A:1-85
2GLUTAREDOXIN_1PS00195 Glutaredoxin active site.GLRX1_ECOLI5-20  1A:5-20

(-) Exons   (0, 0)

(no "Exon" information available for 1QFN)

(-) Sequences/Alignments

NMR Structure
   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:85
 aligned with GLRX1_ECOLI | P68688 from UniProtKB/Swiss-Prot  Length:85

    Alignment length:85
                                    10        20        30        40        50        60        70        80     
          GLRX1_ECOLI     1 MQTVIFGRSGCPYCVRAKDLAEKLSNERDDFQYQYVDIRAEGITKEDLQQKAGKPVETVPQIFVDQQHIGGYTDFAAWVKENLDA  85
               SCOP domains d1qfna_ A: Glutaredoxin (Grx, thioltransferase)                                       SCOP domains
               CATH domains 1qfnA00 A:1-85 Glutaredoxin                                                           CATH domains
               Pfam domains --Glutaredoxin-1qfnA01 A:3-69                                        ---------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh....eeeee........hhhhhhhh.........eee.......hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) GLUTAREDOXIN_2  PDB: A:1-85 UniProt: 1-85                                             PROSITE (1)
                PROSITE (2) ----GLUTAREDOXIN_1  ----------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 1qfn A   1 MQTVIFGRSGCPYSVRAKDLAEKLSNERDDFQYQYVDIRAEGITKEDLQQKAGKPVETVPQIFVDQQHIGGYTDFAAWVKENLDA  85
                                    10        20        30        40        50        60        70        80     

Chain B from PDB  Type:PROTEIN  Length:25
 aligned with RIR1_ECOLI | P00452 from UniProtKB/Swiss-Prot  Length:761

    Alignment length:25
                                   746       756     
           RIR1_ECOLI   737 GAEDAQDDLVPSIQDDGCESGACKI 761
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ......................... Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                 1qfn B 126 GAEDAQDDLVPSIQDDGSESGACKI 150
                                   135       145     

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (16, 18)

NMR Structure(hide GO term definitions)
Chain A   (GLRX1_ECOLI | P68688)
molecular function
    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: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:0009263    deoxyribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    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:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

Chain B   (RIR1_ECOLI | P00452)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0004748    ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor    Catalysis of the reaction: 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin. Thioredoxin disulfide is the oxidized form of thioredoxin.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0009263    deoxyribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0015949    nucleobase-containing small molecule interconversion    The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005971    ribonucleoside-diphosphate reductase complex    An enzyme complex composed of 2-4 or more subunits, which usually contains nonheme iron and requires ATP for catalysis. Catalyzes the formation of 2'-deoxyribonucleoside diphosphate from ribonucleoside diphosphate, using either thioredoxin disulfide or glutaredoxin disulfide as an acceptor.

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    Val A:59 - Pro A:60   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLRX1_ECOLI | P686881ego 1egr 1grx 1upy 1upz 1uq0 1uq1 1uq2 1uq3 1uq6 1uq7 1uqh 1uqn
        RIR1_ECOLI | P004521r1r 1rlr 2r1r 2x0x 2xak 2xap 2xav 2xaw 2xax 2xay 2xaz 2xo4 2xo5 3r1r 3uus 4erm 4erp 4r1r 5cns 5cnt 5cnu 5cnv 5r1r 6r1r 7r1r

(-) Related Entries Specified in the PDB File

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