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(-) Description

Title :  CRYSTAL STRUCTURE OF MANGANESE SUBSTITUTED R2-D84E (D84E MUTANT OF THE R2 SUBUNIT OF E. COLI RIBONUCLEOTIDE REDUCTASE)
 
Authors :  W. C. Voegtli, M. Sommerhalter, J. Baldwin, L. Saleh, J. M. Bollinger Jr. , A. C. Rosenzweig
Date :  09 Jun 03  (Deposition) - 13 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Four-Helix Bundle, Diiron Center, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. C. Voegtli, M. Sommerhalter, L. Saleh, J. Baldwin, J. M. Bollinger Jr. , A. C. Rosenzweig
Variable Coordination Geometries At The Diiron(Ii) Active Site Of Ribonucleotide Reductase R2.
J. Am. Chem. Soc. V. 125 15822 2003
PubMed-ID: 14677973  |  Reference-DOI: 10.1021/JA0370387
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BETA CHAIN
    Chains: A, B
    EC Number: 1.17.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RIR2
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: RIBONUCLEOTIDE REDUCTASE 1, B2 PROTEIN, R2 PROTEIN

 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
01AC1SOFTWAREGLU A:84 , GLU A:115 , HIS A:118 , GLU A:238BINDING SITE FOR RESIDUE MN A 501
02AC2SOFTWARETRP A:111 , GLU A:115 , GLU A:204 , GLU A:238 , HIS A:241BINDING SITE FOR RESIDUE MN A 502
03AC3SOFTWAREGLU B:84 , GLU B:115 , HIS B:118 , GLU B:238BINDING SITE FOR RESIDUE MN B 503
04AC4SOFTWARETRP B:111 , GLU B:115 , GLU B:204 , GLU B:238 , HIS B:241BINDING SITE FOR RESIDUE MN B 504
05AC5SOFTWARETYR A:194 , ALA A:265 , CYS A:272BINDING SITE FOR RESIDUE HG A 601
06AC6SOFTWARETYR A:157 , CYS A:196 , VAL A:200 , HG A:610BINDING SITE FOR RESIDUE HG A 602
07AC7SOFTWAREVAL A:210 , CYS A:214BINDING SITE FOR RESIDUE HG A 603
08AC8SOFTWARETYR B:156 , TYR B:157 , CYS B:196 , VAL B:200 , HG B:612BINDING SITE FOR RESIDUE HG B 604
09AC9SOFTWARETYR B:194 , CYS B:268 , CYS B:272BINDING SITE FOR RESIDUE HG B 605
10BC1SOFTWARETYR B:194 , HOH B:806BINDING SITE FOR RESIDUE HG B 606
11BC2SOFTWAREVAL B:210 , ALA B:213 , CYS B:214 , HG B:613BINDING SITE FOR RESIDUE HG B 607
12BC3SOFTWARELYS B:284 , CYS B:305 , GLU B:309 , HG B:611BINDING SITE FOR RESIDUE HG B 608
13BC4SOFTWARETYR A:194 , LEU A:195 , CYS A:268 , CYS A:272BINDING SITE FOR RESIDUE HG A 609
14BC5SOFTWARETYR A:157 , CYS A:196 , VAL A:200 , HG A:602BINDING SITE FOR RESIDUE HG A 610
15BC6SOFTWARECYS B:305 , GLN B:306 , GLU B:309 , HG B:608BINDING SITE FOR RESIDUE HG B 611
16BC7SOFTWARETYR B:157 , CYS B:196 , VAL B:200 , HG B:604BINDING SITE FOR RESIDUE HG B 612
17BC8SOFTWAREASN B:76 , VAL B:210 , CYS B:214 , LEU B:290 , HG B:607BINDING SITE FOR RESIDUE HG B 613
18BC9SOFTWARECYS A:305 , GLU A:309BINDING SITE FOR RESIDUE HG A 614

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PM2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PM2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PM2)

(-) 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 1PM2)

(-) 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:339
 aligned with RIR2_ECOLI | P69924 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:339
                                    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         
           RIR2_ECOLI     2 AYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWL 340
               SCOP domains d1pm2a_ A: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1pm2A00 A:1-339 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................hhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh............hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------RIBORED_SMALL    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pm2 A   1 AYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLESIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFNTRSNPIPWINTWL 339
                                    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         


Chain B from PDB  Type:PROTEIN  Length:339
 aligned with RIR2_ECOLI | P69924 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:339
                                    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         
           RIR2_ECOLI     2 AYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLDSIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFQTRSNPIPWINTWL 340
               SCOP domains d1pm2b_ B: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1pm2B00 B:1-339 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                                                                 CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ribonuc_red_sm-1pm2B01 B:181-335                                                                                                                           ---- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ribonuc_red_sm-1pm2B02 B:181-335                                                                                                                           ---- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ribonuc_red_sm-1pm2B03 B:181-335                                                                                                                           ---- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Ribonuc_red_sm-1pm2B04 B:181-335                                                                                                                           ---- Pfam domains (4)
         Sec.struct. author ................................hhhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh............hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------RIBORED_SMALL    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pm2 B   1 AYTTFSQTKNDQLKEPMFFGQPVNVARYDQQKYDIFEKLIEKQLSFFWRPEEVDVSRDRIDYQALPEHEKHIFISNLKYQTLLESIQGRSPNVALLPLISIPELETWVETWAFSETIHSRSYTHIIRNIVNDPSVVFDDIVTNEQIQKRAEGISSYYDELIEMTSYWHLLGEGTHTVNGKTVTVSLRELKKKLYLCLMSVNALEAIRFYVSFACSFAFAERELMEGNAKIIRLIARDEALHLTGTQHMLNLLRSGADDPEMAEIAEECKQECYDLFVQAAQQEKDWADYLFRDGSMIGLNKDILCQYVEYITNIRMQAVGLDLPFNTRSNPIPWINTWL 339
                                    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
   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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  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 1jpr 1jqc 1mrr 1mxr 1pfr 1pim 1piu 1piy 1piz 1pj0 1pj1 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

1pim DITHIONITE REDUCED E. COLI RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT, D84E MUTANT'
1piz RIBONUCLEOTIDE REDUCTASE R2 D84E MUTANT SOAKED WITH FERROUS IONS AT NEUTRAL PH