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(-) Description

Title :  HUMAN RIBONUCLEOTIDE REDUCTASE, SUBUNIT M2 B
 
Authors :  M. Welin, M. Moche, J. Andersson, C. H. Arrowsmith, H. Berglund, R. D. Bu R. Collins, L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Gras M. Hammarstrom, M. D. Herman, A. Johansson, I. Johansson, A. Kallas, T. Karlberg, T. Kotenyova, L. Lehtio, M. E. Nilsson, T. Nyman, C. Perss J. Sagemark, H. Schueler, L. Svensson, A. G. Thorsell, L. Tresaugues, S. Van Den Berg, J. Weigelt, M. Wikstrom, P. Nordlund, Structural G Consortium (Sgc)
Date :  31 May 08  (Deposition) - 15 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Replication, De Novo Pathway, Nucleotide Metabolism, Ribonucleotide Reductase, Rnr, Iron, P53R2, Casp8, Nucleus, Metal-Binding, Oxidoreductase, Dna Damage, Dna Repair, Iron Binding, Subunit M2 B (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Welin, M. Moche, C. H. Arrowsmith, H. Berglund, R. D. Busam, R. Collins, L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, M. D. Herman, A. Johansson, I. Johansson A. Kallas, T. Karlberg, T. Kotenyova, L. Lehtio, M. E. Nilsson, T. Nyman, C. Persson, J. Sagemark, H. Schueler, L. Svensson, A. G. Thorsell, L. Tresaugues, S. Van Den Berg, J. Weigelt, M. Wikstrom, P. Nordlund
Human Ribonucleotide Reductase, Subunit M2 B
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT M2 B
    ChainsA, B
    EC Number1.17.4.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 20-322
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTP53-INDUCIBLE RIBONUCLEOTIDE REDUCTASE M2 B, P53-INDUCIBLE RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT 2-LIKE PROTEIN, P53R2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:131 , GLU A:194 , GLU A:228 , HIS A:231BINDING SITE FOR RESIDUE FE A1313
2AC2SOFTWAREGLU B:131 , GLU B:194 , GLU B:228 , HIS B:231BINDING SITE FOR RESIDUE FE B1315

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:45 -Pro A:46
2Phe B:45 -Pro B:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (10, 20)

Asymmetric/Biological Unit (10, 20)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_076280P33SRIR2B_HUMANUnclassified387906892A/BP33S
02UniProtVAR_046217W64RRIR2B_HUMANDisease (MTDPS8A)515726182A/BW64R
03UniProtVAR_065122R110HRIR2B_HUMANDisease (MTDPS8B)267607025A/BR110H
04UniProtVAR_025699V115LRIR2B_HUMANUnclassified  ---A/BV115L
05UniProtVAR_065123R121HRIR2B_HUMANDisease (MTDPS8B)267607024A/BR121H
06UniProtVAR_046219E194GRIR2B_HUMANDisease (MTDPS8A)515726191A/BE194G
07UniProtVAR_046220E194KRIR2B_HUMANDisease (MTDPS8A)121918308A/BE194K
08UniProtVAR_046221I224SRIR2B_HUMANDisease (MTDPS8A)515726196A/BI224S
09UniProtVAR_046222C236FRIR2B_HUMANDisease (MTDPS8A)121918309A/BC236F
10UniProtVAR_046223M282IRIR2B_HUMANDisease (MTDPS8A)182614164A/BM282I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBORED_SMALLPS00368 Ribonucleotide reductase small subunit signature.RIR2B_HUMAN130-146
 
  2A:130-146
B:130-146

(-) Exons   (0, 0)

(no "Exon" information available for 2VUX)

(-) 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:272
 aligned with RIR2B_HUMAN | Q7LG56 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:283
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309   
          RIR2B_HUMAN    30 NEEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFM 312
               SCOP domains d2vuxa_      A: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........-----......hhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh------hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
             SAPs(SNPs) (1) ---S------------------------------R---------------------------------------------H----L-----H------------------------------------------------------------------------G-----------------------------S-----------F---------------------------------------------I------------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------K---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------------------------------------------------------------RIBORED_SMALL    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vux A  30 NEEPLLRK-----VIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAAS------NLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFM 312
                                   | -   |    49        59        69        79        89        99      |109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309   
                                  37    43                                                      99    106                                                                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:255
 aligned with RIR2B_HUMAN | Q7LG56 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:284
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310    
          RIR2B_HUMAN    31 EEPLLRKSSRRFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKREFLFNAIETMPYVKKKADWALRWIADRKSTFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFMEN 314
               SCOP domains d2vuxb_    B: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Ribonu   c_red_sm-2vuxB01 B:32-313                                                                                                                                                                                                                                                        - Pfam domains (1)
           Pfam domains (2) -Ribonu   c_red_sm-2vuxB02 B:32-313                                                                                                                                                                                                                                                        - Pfam domains (2)
         Sec.struct. author .hhhhh.---........hhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh------...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh----------hhhhhhhhh----------hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhh...........hhhhh. Sec.struct. author
             SAPs(SNPs) (1) --S------------------------------R---------------------------------------------H----L-----H------------------------------------------------------------------------G-----------------------------S-----------F---------------------------------------------I-------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------K------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE ---------------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vux B  31 EEPLLRK---RFVIFPIQYPDIWKMYKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFA------NENLVERFSQEVQVPEARCFYGFQILIENVHSEMYSLLIDTYIRDPKKR----------PYVKKKADW----------TFGERVVAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFQYLVNKPSEERVREIIVDAVKIEQEFLTEALPVGLIGMNCILMKQYIEFVADRLLVELGFSKVFQAENPFDFMEN 314
                                  |  -|       50        60        70        80        90      |  -   |   110       120       130       140       150 |       -  |    170|        - |     190       200       210       220       230       240       250       260       270       280       290       300       310    
                                 37  41                                                      97    104                                             152        163     171        182                                                                                                                                    

   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 2VUX)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RIR2B_HUMAN | Q7LG56)
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: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:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    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:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    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:0009200    deoxyribonucleoside triphosphate metabolic process    The chemical reactions and pathways involving a deoxyribonucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with triphosphate 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:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0006264    mitochondrial DNA replication    The process in which new strands of DNA are synthesized in the mitochondrion.
    GO:1902254    negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator    Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway by p53 class mediator.
    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.
    GO:0003014    renal system process    A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila).
    GO:0014075    response to amine    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 an amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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)

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        RIR2B_HUMAN | Q7LG563hf1 4djn

(-) Related Entries Specified in the PDB File

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