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(-) Description

Title :  STRUCTURE OF THE RIBONUCLEOTIDE REDUCTASE RNR4 HOMODIMER FROM SACCHAROMYCES CEREVISIAE
 
Authors :  M. Sommerhalter, W. C. Voegtli, D. L. Perlstein, J. Ge, J. Stubbe, A. C. Rosenzweig
Date :  09 Mar 04  (Deposition) - 10 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sommerhalter, W. C. Voegtli, D. L. Perlstein, J. Ge, J. Stubbe, A. C. Rosenzweig
Structures Of The Yeast Ribonucleotide Reductase Rnr2 And Rnr4 Homodimers.
Biochemistry V. 43 7736 2004
PubMed-ID: 15196016  |  Reference-DOI: 10.1021/BI049510M
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SMALL CHAIN 2
    Chains: A, B
    EC Number: 1.17.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RNR4, YGR180C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT 2

 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
1HG4Ligand/IonMERCURY (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:194 , CYS A:217BINDING SITE FOR RESIDUE HG A 501
2AC2SOFTWARECYS A:228BINDING SITE FOR RESIDUE HG A 502
3AC3SOFTWARETYR B:194 , CYS B:217BINDING SITE FOR RESIDUE HG B 503
4AC4SOFTWARECYS B:228BINDING SITE FOR RESIDUE HG B 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBORED_SMALLPS00368 Ribonucleotide reductase small subunit signature.RIR4_YEAST123-139
 		  2A:123-139
B:123-139

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGR180C1YGR180C.1VII:856306-8552691038RIR4_YEAST1-3453452A:3-325 (gaps)
B:3-325 (gaps)		323
323

(-) 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:314
 aligned with RIR4_YEAST | P49723 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:323
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322   
           RIR4_YEAST     3 AHNQFLKTFQKERHDMKEAEKDEILLMENSRRFVMFPIKYHEIWAAYKKVEASFWTAEEIELAKDTEDFQKLTDDQKTYIGNLLALSISSDNLVNKYLIENFSAQLQNPEGKSFYGFQIMMENIYSEVYSMMVDAFFKDPKNIPLFKEIANLPEVKHKAAFIERWISNDDSLYAERLVAFAAKEGIFQAGNYASMFWLTDKKIMPGLAMANRNICRDRGAYTDFSCLLFAHLRTKPNPKIIEKIITEAVEIEKEYYSNSLPVEKFGMDLKSIHTYIEFVADGLLQGFGNEKYYNAVNPFEFMEDVATAGKTTFFEKKVSDYQK 325
               SCOP domains d1smsa_ A: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1smsA00 A:3-325 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh....hhhhhhhhhhhhhhh............hhhhhhhhhhhhhh..hhhhh.....hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.................---------hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-325 (gaps) UniProt: 1-345 [INCOMPLETE]                                                                                                                                                                                                                                                                           Transcript 1
                 1sms A   3 AHNQFLKTFQKERHDMKEAEKDEILLMENSRRFVMFPIKYHEIWAAYKKVEASFWTAEEIELAKDTEDFQKLTDDQKTYIGNLLALSISSDNLVNKYLIENFSAQLQNPEGKSFYGFQIMMENIYSEVYSMMVDAFFKDPKNIPLFKEIANLPEVKHKAAFIERWISNDDSLYAERLVAFAAKEGIFQAGNYASMFWLTDKKIMPGLAMANRNICRDRGAYTDFSCLLFAHLRTKPNPKIIEKIITEAVEIEKEYYSNSLPVEKFGMDLKSIHTYIEFVADGLLQGFGNEKYYNAVNPFEFME---------FFEKKVSDYQK 325
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302  |      -  |    322   
                                                                                                                                                                                                                                                                                                                                        305       315          


Chain B from PDB  Type:PROTEIN  Length:314
 aligned with RIR4_YEAST | P49723 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:323
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322   
           RIR4_YEAST     3 AHNQFLKTFQKERHDMKEAEKDEILLMENSRRFVMFPIKYHEIWAAYKKVEASFWTAEEIELAKDTEDFQKLTDDQKTYIGNLLALSISSDNLVNKYLIENFSAQLQNPEGKSFYGFQIMMENIYSEVYSMMVDAFFKDPKNIPLFKEIANLPEVKHKAAFIERWISNDDSLYAERLVAFAAKEGIFQAGNYASMFWLTDKKIMPGLAMANRNICRDRGAYTDFSCLLFAHLRTKPNPKIIEKIITEAVEIEKEYYSNSLPVEKFGMDLKSIHTYIEFVADGLLQGFGNEKYYNAVNPFEFMEDVATAGKTTFFEKKVSDYQK 325
               SCOP domains d1smsb_ B: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1smsB00 B:3-325 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh....hhhhhhhhhhhhhhh............hhhhhhhhhhhhhh..hhhhh.....hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.................---------hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-325 (gaps) UniProt: 1-345 [INCOMPLETE]                                                                                                                                                                                                                                                                           Transcript 1
                 1sms B   3 AHNQFLKTFQKERHDMKEAEKDEILLMENSRRFVMFPIKYHEIWAAYKKVEASFWTAEEIELAKDTEDFQKLTDDQKTYIGNLLALSISSDNLVNKYLIENFSAQLQNPEGKSFYGFQIMMENIYSEVYSMMVDAFFKDPKNIPLFKEIANLPEVKHKAAFIERWISNDDSLYAERLVAFAAKEGIFQAGNYASMFWLTDKKIMPGLAMANRNICRDRGAYTDFSCLLFAHLRTKPNPKIIEKIITEAVEIEKEYYSNSLPVEKFGMDLKSIHTYIEFVADGLLQGFGNEKYYNAVNPFEFME---------FFEKKVSDYQK 325
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302  |      -  |    322   
                                                                                                                                                                                                                                                                                                                                        305       315
   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  (0, 0)

(no "Pfam Domain" information available for 1SMS)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RIR4_YEAST | P49723)
molecular function
    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:0051188    cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of a cofactor, a substance that is required for the activity of an enzyme or other protein.
    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: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)

UniProtKB/Swiss-Prot
        RIR4_YEAST | P49723: 1jk0 1zzd

(-) Related Entries Specified in the PDB File

1jk0 STRUCTURE OF THE RIBONUCLEOTIDE REDUCTASE Y2Y4 (RNR2RNR4) HETERODIMER FROM SACCHAROMYCES CEREVISIAE
1smq STRUCTURE OF THE RIBONUCLEOTIDE REDUCTASE RNR2 HOMODIMER FROM SACCHAROMYCES CEREVISIAE