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(-) Description

Title :  RIBONUCLEOTIDE REDUCTASE CLASS 1B HOLOCOMPLEX R1E,R2F FROM SALMONELLA TYPHIMURIUM
 
Authors :  M. Uppsten, M. Farnegardh, V. Domkin, U. Uhlin
Date :  26 Apr 05  (Deposition) - 17 May 06  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym./Biol. Unit :  E,F,I,J
Keywords :  R1, R2, R1E, R2F, Iron, Class 1B, Holocomplex, Allosteric Regulation, Ribonucleotide Reductase, Atp-Binding, Metal- Binding, Oxidoreductase, Dna Replication, Radical Transfer, Allosteric Enzyme, Asymmetric Complex, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Uppsten, M. Farnegardh, V. Domkin, U. Uhlin
The First Holocomplex Structure Of Ribonucleotide Reductase Gives New Insight Into Its Mechanism Of Action
J. Mol. Biol. V. 359 365 2006
PubMed-ID: 16631785  |  Reference-DOI: 10.1016/J.JMB.2006.03.035

(-) Compounds

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 ALPHA SUBUNIT
    Chains: E, F
    EC Number: 1.17.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Synonym: RIBONUCLEOTIDE REDUCTASE 2, R1E PROTEIN
 
Molecule 2 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 2 BETA SUBUNIT
    Chains: I, J
    EC Number: 1.17.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET24A
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Synonym: RIBONUCLEOTIDE REDUCTASE 2, R2F PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : EFIJ

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1DGT2Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2FE4Ligand/IonFE (III) ION
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDGT E:1700BINDING SITE FOR RESIDUE MG E1701
2AC2SOFTWAREDGT F:1700BINDING SITE FOR RESIDUE MG F1701
3AC3SOFTWAREASP I:67 , GLU I:98 , HIS I:101 , PHE I:162 , GLU I:192BINDING SITE FOR RESIDUE FE I1320
4AC4SOFTWAREGLU I:98 , GLU I:158 , GLU I:192 , HIS I:195BINDING SITE FOR RESIDUE FE I1321
5AC5SOFTWAREASP J:67 , GLU J:98 , HIS J:101 , GLU J:192 , FE J:1288BINDING SITE FOR RESIDUE FE J1287
6AC6SOFTWAREGLU J:98 , GLU J:158 , GLU J:192 , HIS J:195 , FE J:1287BINDING SITE FOR RESIDUE FE J1288
7AC7SOFTWAREASP E:185 , ASN E:186 , MET E:187 , ILE E:190 , ARG E:215 , ILE E:221 , LYS E:222 , MG E:1701 , LYS F:202 , TYR F:244BINDING SITE FOR RESIDUE DGT E1700
8AC8SOFTWARELYS E:202 , TYR E:244 , ASP F:185 , ASN F:186 , MET F:187 , ARG F:215 , ILE F:221 , LYS F:222 , MG F:1701BINDING SITE FOR RESIDUE DGT F1700

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1E:178 -E:415
2F:178 -F:415

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr E:363 -Pro E:364
2Tyr F:363 -Pro F:364

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BQ1)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBORED_SMALLPS00368 Ribonucleotide reductase small subunit signature.RIR4_SALTY97-113
 		  2I:97-113
J:97-113
2RIBORED_LARGEPS00089 Ribonucleotide reductase large subunit signature.RIR3_SALTY566-588
 		  2E:566-588
F:566-588

(-) Exons   (0, 0)

(no "Exon" information available for 2BQ1)

(-) 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 E from PDB  Type:PROTEIN  Length:676
 aligned with RIR3_SALTY | Q08698 from UniProtKB/Swiss-Prot  Length:714

    Alignment length:689
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691         
           RIR3_SALTY    12 ETMDYHALNAMLNLYDKAGHIQFDKDQQAIDAFFATHVRPHSVTFASQHERLGTLVREGYYDDAVLARYDRAFVLRLFEHAHASGFRFQTFLGAWKFYTSYTLKTFDGKRYLEHFEDRVTMVALTLAQGDETLATQLTDEMLSGRFQPATPTFLNCGKQQRGELVSCFLLRIEDNMESIGRAVNSALQLSKRGGGVAFLLSNLREAGAPIKRIENQSSGVIPVMKMLEDAFSYANQLGARQGAGAVYLHAHHPDILRFLDTKRENADEKIRIKTLSLGVVIPDITFRLAKENAQMALFSPYDIQRRYGKPFGDIAISERYDELIADPHVRKTYINARDFFQTLAEIQFESGYPYIMFEDTVNRANPIAGRINMSNLCSEILQVNSASRYDDNLDYTHIGHDISCNLGSLNIAHVMDSPDIGRTVETAIRGLTAVSDMSHIRSVPSIAAGNAASHAIGLGQMNLHGYLAREGIAYGSPEALDFTNLYFYTITWHAVHTSMRLARERGKTFAGFAQSRYASGDYFTQYLQDDWQPKTAKVRALFARSGITLPTREMWLKLRDDVMRYGIYNQNLQAVPPTGSISYINHATSSIHPIVAKIEIRKEGKTGRVYYPAPFMTNENLDMYQDAYDIGPEKIIDTYAEATRHVDQGLSLTLFFPDTATTRDINKAQIYAWRKGIKSLYYIRLRQLA 700
               SCOP domains -d2bq1e1 E:13-174 R1 subunit of ribonucleotide reductase, N-terminal domain                                                                                        d2bq1e2 E:175-699 R1 subunit of ribonucleotide reductase, C-terminal dom     ain                                                                                                                                                                                                                                                                                                                                                                                                                                                             - SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh........hhhhhhhhhhhhhhh.........hhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhh............hhhhhhhhhhhhhh..hhhhhhhhhhhhhh..eeehhhhhhhh...........eeee...hhhhhhhhhhhhhhhhhh..eeeee.hhh................hhhhhhhhhhhhhhh.-----..eeeeeee....hhhhhhhhhh--------...eeeeee.hhhhhhhhhh..eeeeehhhhhhhhhh.hhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhh..eeehhhhhhhh.......................ee.....eee....ee.eeeeeehhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh...hhhhh......hhhhhhhhhhhh....hhhhhhhhhhhhhhhh.............hhhhhh............eeee.......eeee.............hhhhhhhhhhhhhhhhhhhhh........ee....hhhhhhhhhhhhhhhh..ee...ee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_LARGE          ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bq1 E  12 ETMDYHALNAMLNLYDKAGHIQFDKDQQAIDAFFATHVRPHSVTFASQHERLGTLVREGYYDDAVLARYDRAFVLRLFEHAHASGFRFQTFLGAWKFYTSYTLKTFDGKRYLEHFEDRVTMVALTLAQGDETLATQLTDEMLSGRFQPATPTFLNCGKQQRGELVSCFLLRIEDNMESIGRAVNSALQLSKRGGGVAFLLSNLREAGAPIKRIENQSSGVIPVMKMLEDAFSYAN-----QGAGAVYLHAHHPDILRFLDTKR--------IKTLSLGVVIPDITFRLAKENAQMALFSPYDIQRRYGKPFGDIAISERYDELIADPHVRKTYINARDFFQTLAEIQFESGYPYIMFEDTVNRANPIAGRINMSNLCSEILQVNSASRYDDNLDYTHIGHDISCNLGSLNIAHVMDSPDIGRTVETAIRGLTAVSDMSHIRSVPSIAAGNAASHAIGLGQMNLHGYLAREGIAYGSPEALDFTNLYFYTITWHAVHTSMRLARERGKTFAGFAQSRYASGDYFTQYLQDDWQPKTAKVRALFARSGITLPTREMWLKLRDDVMRYGIYNQNLQAVPPTGSISYINHATSSIHPIVAKIEIRKEGKTGRVYYPAPFMTNENLDMYQDAYDIGPEKIIDTYAEATRHVDQGLSLTLFFPDTATTRDINKAQIYAWRKGIKSLYYIRLRQLA 700
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    |    -|      261       271  |      - |     291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691         
                                                                                                                                                                                                                                                                    246   252                   274      283                                                                                                                                                                                                                                                                                                                                                                                                                                 


Chain F from PDB  Type:PROTEIN  Length:685
 aligned with RIR3_SALTY | Q08698 from UniProtKB/Swiss-Prot  Length:714

    Alignment length:690
                                    20        30        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       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700
           RIR3_SALTY    11 QETMDYHALNAMLNLYDKAGHIQFDKDQQAIDAFFATHVRPHSVTFASQHERLGTLVREGYYDDAVLARYDRAFVLRLFEHAHASGFRFQTFLGAWKFYTSYTLKTFDGKRYLEHFEDRVTMVALTLAQGDETLATQLTDEMLSGRFQPATPTFLNCGKQQRGELVSCFLLRIEDNMESIGRAVNSALQLSKRGGGVAFLLSNLREAGAPIKRIENQSSGVIPVMKMLEDAFSYANQLGARQGAGAVYLHAHHPDILRFLDTKRENADEKIRIKTLSLGVVIPDITFRLAKENAQMALFSPYDIQRRYGKPFGDIAISERYDELIADPHVRKTYINARDFFQTLAEIQFESGYPYIMFEDTVNRANPIAGRINMSNLCSEILQVNSASRYDDNLDYTHIGHDISCNLGSLNIAHVMDSPDIGRTVETAIRGLTAVSDMSHIRSVPSIAAGNAASHAIGLGQMNLHGYLAREGIAYGSPEALDFTNLYFYTITWHAVHTSMRLARERGKTFAGFAQSRYASGDYFTQYLQDDWQPKTAKVRALFARSGITLPTREMWLKLRDDVMRYGIYNQNLQAVPPTGSISYINHATSSIHPIVAKIEIRKEGKTGRVYYPAPFMTNENLDMYQDAYDIGPEKIIDTYAEATRHVDQGLSLTLFFPDTATTRDINKAQIYAWRKGIKSLYYIRLRQLA 700
               SCOP domains --d2bq1f1 F:13-174 R1 subunit of ribonucleotide reductase, N-terminal domain                                                                                        d2bq1f2 F:175-699 R1 subunit of ribonucleotide reductase, C-terminal dom     ain                                                                                                                                                                                                                                                                                                                                                                                                                                                             - SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhh............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..eeehhhhhh............eeeee...hhhhhhhhhhhhhhhhh...eeeee....................hhhhhhhhhhhhhhh.-----...eeeeee....hhhhhh................eeeee..hhhhhhhhh..eeeeehhhhhhhhhh.hhhhh....hhhhhhhh....eeeeehhhhhhhhhhhhhhhh..eeehhhhhhhhh......................ee.....eee....ee..eeeehhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh..ee...hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh..............hhhhhhhhhhhh......hhhhhhhhhhhhhh.............hhhhh.............eeee.......eeee.......hhhhh.hhhhhhhhhhhhhhhhhhhhh.......eee....hhhhhhhhhhhhhhhh..ee..eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_LARGE          ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bq1 F  11 QETMDYHALNAMLNLYDKAGHIQFDKDQQAIDAFFATHVRPHSVTFASQHERLGTLVREGYYDDAVLARYDRAFVLRLFEHAHASGFRFQTFLGAWKFYTSYTLKTFDGKRYLEHFEDRVTMVALTLAQGDETLATQLTDEMLSGRFQPATPTFLNCGKQQRGELVSCFLLRIEDNMESIGRAVNSALQLSKRGGGVAFLLSNLREAGAPIKRIENQSSGVIPVMKMLEDAFSYAN-----QGAGAVYLHAHHPDILRFLDTKRENADEKIRIKTLSLGVVIPDITFRLAKENAQMALFSPYDIQRRYGKPFGDIAISERYDELIADPHVRKTYINARDFFQTLAEIQFESGYPYIMFEDTVNRANPIAGRINMSNLCSEILQVNSASRYDDNLDYTHIGHDISCNLGSLNIAHVMDSPDIGRTVETAIRGLTAVSDMSHIRSVPSIAAGNAASHAIGLGQMNLHGYLAREGIAYGSPEALDFTNLYFYTITWHAVHTSMRLARERGKTFAGFAQSRYASGDYFTQYLQDDWQPKTAKVRALFARSGITLPTREMWLKLRDDVMRYGIYNQNLQAVPPTGSISYINHATSSIHPIVAKIEIRKEGKTGRVYYPAPFMTNENLDMYQDAYDIGPEKIIDTYAEATRHVDQGLSLTLFFPDTATTRDINKAQIYAWRKGIKSLYYIRLRQLA 700
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     |   - |     260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700
                                                                                                                                                                                                                                                                     246   252                                                                                                                                                                                                                                                                                                                                                                                                                                                                


Chain I from PDB  Type:PROTEIN  Length:294
 aligned with RIR4_SALTY | P17424 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:314
                                    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       295       305       315    
           RIR4_SALTY     6 ISAINWNKIQDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLSAAEQQLTIRVFTGLTLLDTIQNIAGAPSLMADAITPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKEVDAAYAWSEENPPLQRKAQIILAHYVSDEPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQIALQKLSAIEREELKLFALDLLMELYDNEIRYTEALYAETGWVNDVKAFLCYNANKALMNLGYEALFPPEMADVNPAILAALSPNADENHDFFSGSGSSYVMGKTVETEDEDWNF 319
               SCOP domains d2bq1i1 I:6-288 Ribonucleotide reductase R2                                                                                                                                                                                                                                                ------------------------------- SCOP domains
               CATH domains 2bq1I01 I:6-288 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                        ------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...............hhhhhhhh..--------------------........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------RIBORED_SMALL    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bq1 I   6 ISAINWNKIQDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLSAAEQQLTIRVFTGLTLLDTIQNIAGAPSLMADAITPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKEVDAAYAWSEENPPLQRKAQIILAHYVSDEPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQIALQKLSAIEREELKLFALDLLMELYDNEIRYTEALYAETGWVNDVKAFLCYNANKALMNLGYEALFPPEMADVNPAILAALSP--------------------TVETEDEDWNF 319
                                    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  |      -         -   |   315    
                                                                                                                                                                                                                                                                                                                    288                  309          


Chain J 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 d2bq1j1 J:6-286 Ribonucleotide reductase R2                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2bq1J00 J:6-286 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhh...........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------RIBORED_SMALL    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bq1 J   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  (3, 6)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BQ1)

(-) Gene Ontology  (12, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E,F   (RIR3_SALTY | Q08698)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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.

Chain I,J   (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)

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        RIR3_SALTY | Q08698: 1pem 1peo 1peq 1peu
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(-) Related Entries Specified in the PDB File

1pem RIBONUCLEOTIDE REDUCTASE PROTEIN R1E FROM SALMONELLATYPHIMURIUM
1peo RIBONUCLEOTIDE REDUCTASE PROTEIN R1E FROM SALMONELLATYPHIMURIUM
1peq RIBONUCLEOTIDE REDUCTASE PROTEIN R1E FROM SALMONELLATYPHIMURIUM
1peu RIBONUCLEOTIDE REDUCTASE PROTEIN R1E FROM SALMONELLATYPHIMURIUM
1r2f RIBONUCLEOTIDE REDUCTASE R2F PROTEIN FROM SALMONELLATYPHIMURIUM
2r2f RIBONUCLEOTIDE REDUCTASE R2F PROTEIN FROM SALMONELLATYPHIMURIUM (OXIDIZED)