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(-) Description

Title :  PLASMODIUM VIVAX RIBONUCLEOTIDE REDUCTASE SUBUNIT R2 (PV086155)
 
Authors :  A. Dong, W. Tempel, W. Qiu, J. Lew, A. K. Wernimont, Y. H. Lin, A. Hassanali, M. Melone, Y. Zhao, P. Nordlund, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, M. Sundstrom, A. Bochkarev, R. Hui, J. D. Artz, M. Amani, Structural Genomics Consortium (Sgc)
Date :  29 Nov 06  (Deposition) - 12 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Small Subunit Ribonucleotide Reductase, Oxidoreductase, Dna Replication, R2, Iron, Diiron, Radical, R2 Subunit, Metal- Binding, Ribonucleotide Reductase, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dong, W. Tempel, W. Qiu, J. Lew, A. K. Wernimont, Y. H. Lin, A. Hassanali, M. Melone, Y. Zhao, P. Nordlund, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, M. Sundstrom, A. Bochkarev, R. Hui, J. D. Artz, M. Amani
Crystal Structure Of Plasmodium Vivax Ribonucleotide Reductase Subunit R2 (Pv086155)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEOTIDE REDUCTASE SUBUNIT R2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15-TEV-LIC DERIVED FROM PET15
    Expression System Strain: BL21 ROSETTA-R3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: MALARIA PARASITE P. VIVAX
    Organism Scientific: PLASMODIUM VIVAX
    Organism Taxid: 5855

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2UNX2Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:125 , GLU A:129 , GLU A:191 , GLU A:225 , HIS A:228BINDING SITE FOR RESIDUE FE A 1000
2AC2SOFTWAREGLU B:129 , GLU B:191 , GLU B:225 , HIS B:228BINDING SITE FOR RESIDUE FE B 1001
3AC3SOFTWARETYR A:47 , PRO A:48 , ASP A:49 , VAL A:50BINDING SITE FOR RESIDUE UNX A 2001
4AC4SOFTWARESER A:133 , GLU A:134 , SER A:137 , LYS B:120BINDING SITE FOR RESIDUE UNX A 2002

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:264 -A:269
2B:264 -B:269

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:43 -Pro A:44
2Tyr B:43 -Pro B:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O1Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O1Z)

(-) Exons   (0, 0)

(no "Exon" information available for 2O1Z)

(-) 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:288
 aligned with A5K1H0_PLAVS | A5K1H0 from UniProtKB/TrEMBL  Length:349

    Alignment length:295
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307     
         A5K1H0_PLAVS    18 KKFSDLQKSKEANEKILSKETDRFTLYPILYPDVWDFYKKAEASFWTAEEIDLSSDLKDFEKLNDNEKHFIKHVLAFFAASDGIVLENLASKFLRQVKITEAKKFYAFQIAVENIHSETYSLLIDNYIKDEKERMNLFHAIENIPAVKNKALWAAKWINDTNSFAERIVANACVEGILFSGSFCAIFWFKKQNKLHGLTFSNELISRDEGLHTDFNCLIYSLLENKLPEEVVQNIVKEAVEVERSFICESLPCDLIGMNSRLMSQYIEFVADRLLECLGSPKIFHAKNPFNWMDL 312
               SCOP domains d2o1za_ A: automated matches                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2o1zA01 A:17-295 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                   ---------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh-------hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o1z A  17 KKFSDLQKSKEANEKILSKETDRFTLYPILYPDVWDFYKKAEASFWTAEEIDLSSDLKDFEKLNDNEKHFIKHVLAFFAAS-------LASKFLRQVKITEAKKFYAFQIAVENIHSETYSLLIDNYIKDEKERMNLFHAIENIPAVKNKALWAAKWINDTNSFAERIVANACVEGILFSGSFCAIFWFKKQNKLHGLTFSNELISRDEGLHTDFNCLIYSLLENKLPEEVVQNIVKEAVEVERSFICESLPCDLIGMNSRLMSQYIEFVADRLLECLGSPKIFHAKNPFNWMDL 311
                                    26        36        46        56        66        76        86        96|      106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306     
                                                                                                           97     105                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:279
 aligned with A5K1H0_PLAVS | A5K1H0 from UniProtKB/TrEMBL  Length:349

    Alignment length:286
                                    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       294       304      
         A5K1H0_PLAVS    25 KSKEANEKILSKETDRFTLYPILYPDVWDFYKKAEASFWTAEEIDLSSDLKDFEKLNDNEKHFIKHVLAFFAASDGIVLENLASKFLRQVKITEAKKFYAFQIAVENIHSETYSLLIDNYIKDEKERMNLFHAIENIPAVKNKALWAAKWINDTNSFAERIVANACVEGILFSGSFCAIFWFKKQNKLHGLTFSNELISRDEGLHTDFNCLIYSLLENKLPEEVVQNIVKEAVEVERSFICESLPCDLIGMNSRLMSQYIEFVADRLLECLGSPKIFHAKNPFNWM 310
               SCOP domains d2o1zb_ B: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2o1zB01 B:24-295 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                            -------------- CATH domains
           Pfam domains (1) ------Ribonuc_red_sm-2o1zB01 B:30-309                                                                                                                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) ------Ribonuc_red_sm-2o1zB02 B:30-309                                                                                                                                                                                                                                                          Pfam domains (2)
         Sec.struct. author .......................hhhhhhhhhhhhhh..hhhhh.hhhhhhhhh--hhhhhhhhhhhhhhhhhh...---hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.....--...hhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o1z B  24 KSKEANEKILSKETDRFTLYPILYPDVWDFYKKAEASFWTAEEIDLSSDLKDFE--NDNEKHFIKHVLAFFAASDGI---NLASKFLRQVKITEAKKFYAFQIAVENIHSETYSLLIDNYIKDEKERMNLFHAIENIPAVKNKALWAAKWINDTNSFAERIVANACVEGILFSGSFCAIFWFKKQNKLHGLTFSNELISRDEGLHTDFNCLIYSLLENKLPEEVVQNIVKEAVEVERSFICESLPC--IGMNSRLMSQYIEFVADRLLECLGSPKIFHAKNPFNWM 309
                                    33        43        53        63        73   |  | 83        93      |  -|      113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263     | 273       283       293       303      
                                                                                77 80                 100 104                                                                                                                                                                  269  |                                     
                                                                                                                                                                                                                                                                                  272
   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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A5K1H0_PLAVS | A5K1H0)
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.
biological process
    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: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.

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