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(-) Description

Title :  MN SUBSTITUTED RIBONUCLEOTIDE REDUCTASE R2 FROM E. COLI OXIDIZED BY NITRIC OXIDE
 
Authors :  M. Hogbom, M. E. Andersson, P. Nordlund
Date :  03 Aug 01  (Deposition) - 15 Aug 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Radical Protein, Mn Substituted, Oxidized By No, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hogbom, M. E. Andersson, P. Nordlund
Crystal Structures Of Oxidized Dinuclear Manganese Centres In Mn-Substituted Class I Ribonucleotide Reductase From Escherichia Coli: Carboxylate Shifts With Implications For O2 Activation And Radical Generation.
J. Biol. Inorg. Chem. V. 6 315 2001
PubMed-ID: 11315567  |  Reference-DOI: 10.1007/S007750000205
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN R2 OF RIBONUCLEOTIDE REDUCTASE
    Chains: A, B
    EC Number: 1.17.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTB2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BETA CHAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric/Biological Unit (2, 18)
No.NameCountTypeFull Name
1HG14Ligand/IonMERCURY (II) ION
2MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP B:84 , GLU B:115 , HIS B:118 , GLU B:238 , MN B:402 , HOH B:984 , HOH B:1077BINDING SITE FOR RESIDUE MN B 401
02AC2SOFTWAREGLU B:115 , GLU B:204 , GLU B:238 , HIS B:241 , MN B:401 , HOH B:984BINDING SITE FOR RESIDUE MN B 402
03AC3SOFTWAREASP A:84 , GLU A:115 , HIS A:118 , GLU A:238 , MN A:404 , HOH A:1031BINDING SITE FOR RESIDUE MN A 403
04AC4SOFTWAREGLU A:115 , GLU A:204 , GLU A:238 , HIS A:241 , MN A:403 , HOH A:964BINDING SITE FOR RESIDUE MN A 404
05AC5SOFTWARETYR A:157 , CYS A:196 , VAL A:200 , HOH A:916 , HOH A:950BINDING SITE FOR RESIDUE HG A 901
06AC6SOFTWARETYR B:157 , CYS B:196 , VAL B:200 , HG B:904BINDING SITE FOR RESIDUE HG B 902
07AC7SOFTWARETYR B:194 , LEU B:195 , CYS B:268 , CYS B:272 , HOH B:920BINDING SITE FOR RESIDUE HG B 903
08AC8SOFTWARETYR B:156 , TYR B:157 , CYS B:196 , VAL B:200 , HG B:902 , HOH B:936BINDING SITE FOR RESIDUE HG B 904
09AC9SOFTWAREILE B:72 , CYS B:214 , PHE B:218 , MET B:296 , HOH B:1202BINDING SITE FOR RESIDUE HG B 906
10BC1SOFTWARETYR A:194 , ALA A:265 , CYS A:272 , HOH A:958BINDING SITE FOR RESIDUE HG A 907
11BC2SOFTWAREVAL A:210 , CYS A:214 , LEU A:304BINDING SITE FOR RESIDUE HG A 909
12BC3SOFTWAREMET B:198 , CYS B:272 , LEU B:275 , PHE B:276 , HOH B:1254BINDING SITE FOR RESIDUE HG B 910
13BC4SOFTWAREVAL B:210 , ALA B:213 , CYS B:214 , LEU B:304 , HG B:912BINDING SITE FOR RESIDUE HG B 911
14BC5SOFTWAREASN B:76 , VAL B:210 , CYS B:214 , TRP B:286 , LEU B:304 , HG B:911 , HOH B:1202BINDING SITE FOR RESIDUE HG B 912
15BC6SOFTWARECYS A:305 , GLN A:306 , GLU A:309 , HOH A:949 , HOH A:1289BINDING SITE FOR RESIDUE HG A 915
16BC7SOFTWARELYS B:284 , CYS B:305 , GLU B:309 , HOH B:953BINDING SITE FOR RESIDUE HG B 916
17BC8SOFTWARETYR B:194 , ALA B:265 , HOH B:920 , HOH B:1071BINDING SITE FOR RESIDUE HG B 917
18BC9SOFTWARELYS B:191 , ILE B:264 , GLU B:267 , CYS B:268BINDING SITE FOR RESIDUE HG B 918

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBORED_SMALLPS00368 Ribonucleotide reductase small subunit signature.RIR2_ECOLI115-131
 		  2A:114-130
B:114-130

(-) Exons   (0, 0)

(no "Exon" information available for 1JPR)

(-) 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:340
 aligned with RIR2_ECOLI | P69924 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:340
                                    11        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
           RIR2_ECOLI     2 AYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWLV 341
               SCOP domains d1jpra_ A: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1jprA00 A:1-340 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh.................hhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..............hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jpr A   1 AYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWLV 340
                                    10        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


Chain B from PDB  Type:PROTEIN  Length:341
 aligned with RIR2_ECOLI | P69924 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:341
                                    11        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 
           RIR2_ECOLI     2 AYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWLVS 342
               SCOP domains d1jprb_ B: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1jprB00 B:1-341 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ribonuc_red_sm-1jprB01 B:181-335                                                                                                                           ------ Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ribonuc_red_sm-1jprB02 B:181-335                                                                                                                           ------ Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ribonuc_red_sm-1jprB03 B:181-335                                                                                                                           ------ Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ribonuc_red_sm-1jprB04 B:181-335                                                                                                                           ------ Pfam domains (4)
         Sec.struct. author ................................hhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh............hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------RIBORED_SMALL    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jpr B   1 AYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWLVS 341
                                    10        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
   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, 4)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RIR2_ECOLI | P69924)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) 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: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: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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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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  1jpr
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  RIR2_ECOLI | P69924
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  1.17.4.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        RIR2_ECOLI | P69924: 1av8 1biq 1jqc 1mrr 1mxr 1pfr 1pim 1piu 1piy 1piz 1pj0 1pj1 1pm2 1r1r 1r65 1rib 1rnr 1rsr 1rsv 1xik 1yfd 2alx 2av8 2r1r 2x0x 2xak 2xap 2xav 2xaw 2xax 2xay 2xaz 2xo4 2xo5 2xof 3r1r 3uus 4erm 4erp 4r1r 5ci2 5ci3 5cns 5cnt 5cnu 5cnv 5r1r 6r1r 7r1r

(-) Related Entries Specified in the PDB File

1jqc 1JQC CONTAINS THE SAME MN SUBSTITUTED PROTEIN OXIDIZED IN ANOTHER WAY (BY HYDROGEN PEROXIDE AND HYDROXYLAMINE)