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(-) Description

Title :  RIBONUCLEOTIDE REDUCTASE DIMANGANESE(II)-NRDF FROM ESCHERICHIA COLI IN COMPLEX WITH REDUCED NRDI WITH A TRAPPED PEROXIDE
 
Authors :  A. K. Boal, J. A. Cotruvo Jr. , J. Stubbe, A. C. Rosenzweig
Date :  19 May 10  (Deposition) - 18 Aug 10  (Release) - 24 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ribonucleotide Reductase, Four-Helix Bundle, Dimanganese Cluster, Flavoprotein, Peroxide, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. K. Boal, J. A. Cotruvo, J. Stubbe, A. C. Rosenzweig
Structural Basis For Activation Of Class Ib Ribonucleotide Reductase.
Science V. 329 1526 2010
PubMed-ID: 20688982  |  Reference-DOI: 10.1126/SCIENCE.1190187

(-) Compounds

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 SUBUNIT BETA
    ChainsB, A
    EC Number1.17.4.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneB2676, JW2651, NRDF, YGAD
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12
    SynonymRIBONUCLEOTIDE REDUCTASE 2, R2F PROTEIN
 
Molecule 2 - PROTEIN NRDI
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneNRDI, YGAO, B2674, JW2649
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2MN4Ligand/IonMANGANESE (II) ION
3PEO2Ligand/IonHYDROGEN PEROXIDE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:67 , GLU B:98 , HIS B:101 , GLU B:158 , GLU B:192 , MN B:321 , HOH B:375BINDING SITE FOR RESIDUE MN B 320
2AC2SOFTWAREGLU B:98 , GLU B:158 , GLU B:192 , HIS B:195 , MN B:320 , HOH B:381BINDING SITE FOR RESIDUE MN B 321
3AC3SOFTWARESER B:159 , LYS B:260 , HOH B:329 , ASN C:83 , ASN C:85BINDING SITE FOR RESIDUE PEO B 322
4AC4SOFTWAREARG B:25 , TYR B:197 , SER C:8 , SER C:9 , SER C:11 , GLU C:12 , ASN C:13 , THR C:14 , PRO C:47 , SER C:48 , TYR C:49 , GLY C:50 , GLY C:51 , GLY C:82 , ASN C:83 , PHE C:86 , ALA C:89 , TYR C:90 , GLY C:91 , LEU C:111 , HOH C:138 , HOH C:143BINDING SITE FOR RESIDUE FMN C 134
5AC5SOFTWAREASP A:67 , GLU A:98 , HIS A:101 , GLU A:158 , GLU A:192 , HOH A:361BINDING SITE FOR RESIDUE MN A 320
6AC6SOFTWAREGLU A:98 , GLU A:158 , GLU A:192 , HIS A:195 , HOH A:334BINDING SITE FOR RESIDUE MN A 321
7AC7SOFTWARESER A:159 , LYS A:260 , ASN A:264 , HOH A:359 , ASN D:83 , ASN D:85BINDING SITE FOR RESIDUE PEO A 322
8AC8SOFTWAREARG A:25 , TYR A:197 , SER D:8 , SER D:9 , SER D:11 , GLU D:12 , ASN D:13 , THR D:14 , PRO D:47 , SER D:48 , TYR D:49 , GLY D:50 , SER D:81 , GLY D:82 , ASN D:83 , PHE D:86 , ALA D:89 , TYR D:90 , GLY D:91 , LEU D:111 , HOH D:136BINDING SITE FOR RESIDUE FMN D 134

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N3B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3N3B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N3B)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBORED_SMALLPS00368 Ribonucleotide reductase small subunit signature.RIR4_ECOLI97-113
 
  2A:97-113
B:97-113

(-) Exons   (0, 0)

(no "Exon" information available for 3N3B)

(-) 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:284
 aligned with RIR4_ECOLI | P37146 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:284
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284    
           RIR4_ECOLI     5 RISAINWNKISDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLTVVEQQLTMRVFTGLTLLDTLQNVIGAPSLMPDALTPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKDVDAAYAWSEENAPLQRKAQIIQQHYRGDDPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQYTDELYAETPWADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALSP 288
               SCOP domains d3n3ba_ A: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n3b A   5 RISAINWNKISDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLTVVEQQLTMRVFTGLTLLDTLQNVIGAPSLMPDALTPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKDVDAAYAWSEENAPLQRKAQIIQQHYRGDDPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQYTDELYAETPWADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALSP 288
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284    

Chain B from PDB  Type:PROTEIN  Length:284
 aligned with RIR4_ECOLI | P37146 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:284
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284    
           RIR4_ECOLI     5 RISAINWNKISDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLTVVEQQLTMRVFTGLTLLDTLQNVIGAPSLMPDALTPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKDVDAAYAWSEENAPLQRKAQIIQQHYRGDDPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQYTDELYAETPWADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALSP 288
               SCOP domains d3n3bb_ B: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Ribonuc_red_sm-3n3bB01 B:5-281                                                                                                                                                                                                                                                       ------- Pfam domains (1)
           Pfam domains (2) Ribonuc_red_sm-3n3bB02 B:5-281                                                                                                                                                                                                                                                       ------- Pfam domains (2)
         Sec.struct. author ...........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh......hhhhhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n3b B   5 RISAINWNKISDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLTVVEQQLTMRVFTGLTLLDTLQNVIGAPSLMPDALTPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKDVDAAYAWSEENAPLQRKAQIIQQHYRGDDPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQYTDELYAETPWADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALSP 288
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284    

Chain C from PDB  Type:PROTEIN  Length:129
 aligned with NRDI_ECOLI | P0A772 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:129
                                    12        22        32        42        52        62        72        82        92       102       112       122         
           NRDI_ECOLI     3 QLVYFSSSSENTQRFIERLGLPAVRIPLNERERIQVDEPYILIVPSYGGGGTAGAVPRQVIRFLNDEHNRALLRGVIASGNRNFGEAYGRAGDVIARKCGVPWLYRFELMGTQSDIENVRKGVTEFWQR 131
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....hhhhhhhhhhh..eee..............eeeeee...........hhhhhhhhhhhhhhh.eeeeeeeehhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n3b C   3 QLVYFSSSSENTQRFIERLGLPAVRIPLNERERIQVDEPYILIVPSYGGGGTAGAVPRQVIRFLNDEHNRALLRGVIASGNRNFGEAYGRAGDVIARKCGVPWLYRFELMGTQSDIENVRKGVTEFWQR 131
                                    12        22        32        42        52        62        72        82        92       102       112       122         

Chain D from PDB  Type:PROTEIN  Length:129
 aligned with NRDI_ECOLI | P0A772 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:129
                                    12        22        32        42        52        62        72        82        92       102       112       122         
           NRDI_ECOLI     3 QLVYFSSSSENTQRFIERLGLPAVRIPLNERERIQVDEPYILIVPSYGGGGTAGAVPRQVIRFLNDEHNRALLRGVIASGNRNFGEAYGRAGDVIARKCGVPWLYRFELMGTQSDIENVRKGVTEFWQR 131
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Flavodoxin_NdrI-3n3bD01 D:5-123                                                                                        -------- Pfam domains (1)
           Pfam domains (2) --Flavodoxin_NdrI-3n3bD02 D:5-123                                                                                        -------- Pfam domains (2)
         Sec.struct. author .eeee....hhhhhhhhhhh..eeee.............eeeeee...........hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n3b D   3 QLVYFSSSSENTQRFIERLGLPAVRIPLNERERIQVDEPYILIVPSYGGGGTAGAVPRQVIRFLNDEHNRALLRGVIASGNRNFGEAYGRAGDVIARKCGVPWLYRFELMGTQSDIENVRKGVTEFWQR 131
                                    12        22        32        42        52        62        72        82        92       102       112       122         

   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  (0, 0)

(no "CATH Domain" information available for 3N3B)

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (14, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RIR4_ECOLI | P37146)
molecular function
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    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: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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

Chain C,D   (NRDI_ECOLI | P0A772)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    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).
biological process
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).

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 Related Entries

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

UniProtKB/Swiss-Prot
        NRDI_ECOLI | P0A7723n39 3n3a
        RIR4_ECOLI | P371463n37 3n38 3n39 3n3a 4m1f

(-) Related Entries Specified in the PDB File

3n37 RIBONUCLEOTIDE REDUCTASE DIMANGANESE(II)-NRDF FROM ESCHERICHIA COLI
3n38 RIBONUCLEOTIDE REDUCTASE NRDF FROM ESCHERICHIA COLI SOAKED WITH FERROUS IONS
3n39 RIBONUCLEOTIDE REDUCTASE DIMANGANESE(II)-NRDF FROM ESCHERICHIA COLI IN COMPLEX WITH NRDI
3n3a RIBONUCLEOTIDE REDUCTASE DIMANGANESE(II)-NRDF FROM ESCHERICHIA COLI IN COMPLEX WITH REDUCED NRDI