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(-) Description

Title :  RIBONUCLEOTIDE REDUCTASE R2F PROTEIN FROM SALMONELLA TYPHIMURIUM
 
Authors :  H. Eklund, M. Eriksson
Date :  24 Aug 98  (Deposition) - 13 Jan 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Reductase, Nucleotide Metabolism, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Eriksson, A. Jordan, H. Eklund
Structure Of Salmonella Typhimurium Nrdf Ribonucleotide Reductase In Its Oxidized And Reduced Forms.
Biochemistry V. 37 13359 1998
PubMed-ID: 9748343  |  Reference-DOI: 10.1021/BI981380S
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (RIBONUCLEOTIDE REDUCTASE R2)
    ChainsA, B
    EC Number1.17.4.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System Cellular LocationCYTOPLASM
    Expression System PlasmidPET24A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificSALMONELLA TYPHIMURIUM
    Organism Taxid602

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1FE4Ligand/IonFE (III) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:67 , GLU A:98 , HIS A:101 , GLU A:192 , FE A:401 , HOH A:562BINDING SITE FOR RESIDUE FE A 400
2AC2SOFTWAREGLU A:98 , GLU A:158 , GLU A:192 , HIS A:195 , FE A:400 , HOH A:562BINDING SITE FOR RESIDUE FE A 401
3AC3SOFTWAREASP B:67 , GLU B:98 , HIS B:101 , GLU B:192 , FE B:403BINDING SITE FOR RESIDUE FE B 402
4AC4SOFTWAREGLU B:98 , GLU B:158 , GLU B:192 , HIS B:195 , FE B:402BINDING SITE FOR RESIDUE FE B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R2F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R2F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R2F)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBORED_SMALLPS00368 Ribonucleotide reductase small subunit signature.RIR4_SALTY97-113
 
  2A:97-113
B:97-113

(-) Exons   (0, 0)

(no "Exon" information available for 1R2F)

(-) Sequences/Alignments

Asymmetric/Biological 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:283
 aligned with RIR4_SALTY | P17424 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:283
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285   
           RIR4_SALTY     6 ISAINWNKIQDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLSAAEQQLTIRVFTGLTLLDTIQNIAGAPSLMADAITPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKEVDAAYAWSEENPPLQRKAQIILAHYVSDEPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQIALQKLSAIEREELKLFALDLLMELYDNEIRYTEALYAETGWVNDVKAFLCYNANKALMNLGYEALFPPEMADVNPAILAALSP 288
               SCOP domains d1r2fa_ A: Ribonucleotide reductase R2                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1r2fA00 A:6-288 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhh....hhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..............hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r2f A   6 ISAINWNKIQDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLSAAEQQLTIRVFTGLTLLDTIQNIAGAPSLMADAITPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKEVDAAYAWSEENPPLQRKAQIILAHYVSDEPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQIALQKLSAIEREELKLFALDLLMELYDNEIRYTEALYAETGWVNDVKAFLCYNANKALMNLGYEALFPPEMADVNPAILAALSP 288
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285   

Chain B from PDB  Type:PROTEIN  Length:281
 aligned with RIR4_SALTY | P17424 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:281
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285 
           RIR4_SALTY     6 ISAINWNKIQDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLSAAEQQLTIRVFTGLTLLDTIQNIAGAPSLMADAITPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKEVDAAYAWSEENPPLQRKAQIILAHYVSDEPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQIALQKLSAIEREELKLFALDLLMELYDNEIRYTEALYAETGWVNDVKAFLCYNANKALMNLGYEALFPPEMADVNPAILAAL 286
               SCOP domains d1r2fb_ B: Ribonucleotide reductase R2                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1r2fB00 B:6-286 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                       CATH domains
           Pfam domains (1) Ribonuc_red_sm-1r2fB01 B:6-281                                                                                                                                                                                                                                                      ----- Pfam domains (1)
           Pfam domains (2) Ribonuc_red_sm-1r2fB02 B:6-281                                                                                                                                                                                                                                                      ----- Pfam domains (2)
         Sec.struct. author ...........hhhhhhhhhhhh....hhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh..hhhhhhhhhhhhhhhhhhh.......hhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------RIBORED_SMALL    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r2f B   6 ISAINWNKIQDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLSAAEQQLTIRVFTGLTLLDTIQNIAGAPSLMADAITPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKEVDAAYAWSEENPPLQRKAQIILAHYVSDEPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQIALQKLSAIEREELKLFALDLLMELYDNEIRYTEALYAETGWVNDVKAFLCYNANKALMNLGYEALFPPEMADVNPAILAAL 286
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285 

   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/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Ferritin (185)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RIR4_SALTY | P17424)
molecular function
    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: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:0009186    deoxyribonucleoside diphosphate metabolic process    The chemical reactions and pathways involving a deoxyribonucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with diphosphate on the sugar.
    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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        RIR4_SALTY | P174242bq1 2r2f

(-) Related Entries Specified in the PDB File

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