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(-) Description

Title :  R2-LIKE LIGAND BINDING MN/FE OXIDASE FROM M. TUBERCULOSIS
 
Authors :  C. S. Andersson, T. A. Jones, M. Hogbom
Date :  04 Sep 08  (Deposition) - 07 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Manganese, Iron, Diiron, Carboxylate, Oxidase, R2, Ligand, Cavity, Monooxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. S. Andersson
A Mycobacterium Tuberculosis Ligand-Binding Mn/Fe Protein Reveals A New Cofactor In A Remodeled R2-Protein Scaffold
Proc. Natl. Acad. Sci. Usa V. 106 5633 2009
PubMed-ID: 19321420  |  Reference-DOI: 10.1073/PNAS.0812971106

(-) Compounds

Molecule 1 - PROBABLE RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE
    Chains: A
    EC Number: 1.17.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCR-T7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NRDB, RV0233
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV
    Synonym: MN/FE LIGAND BINDING OXIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2MN31Ligand/IonMANGANESE (III) ION
3MYR1Ligand/IonMYRISTIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2MN32Ligand/IonMANGANESE (III) ION
3MYR2Ligand/IonMYRISTIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:56 , GLU A:68 , GLU A:101 , VAL A:166 , GLU A:167 , GLU A:202 , PHE A:246 , PHE A:262 , MN3 A:316 , FE A:317 , HOH A:343 , HOH A:483BINDING SITE FOR RESIDUE MYR A 315
2AC2SOFTWAREGLU A:68 , GLU A:101 , HIS A:104 , MYR A:315 , FE A:317 , HOH A:343 , HOH A:483BINDING SITE FOR RESIDUE MN3 A 316
3AC3SOFTWAREGLU A:101 , GLU A:167 , GLU A:202 , HIS A:205 , MYR A:315 , MN3 A:316 , HOH A:343BINDING SITE FOR RESIDUE FE A 317

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EE4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EE4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EE4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EE4)

(-) Exons   (0, 0)

(no "Exon" information available for 3EE4)

(-) Sequences/Alignments

Asymmetric 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:289
 aligned with RIR2H_MYCTO | P9WH68 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:289
                                    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         
          RIR2H_MYCTO     2 TRTRSGSLAAGGLNWASLPLKLFAGGNAKFWDPADIDFTRDRADWEKLSDDERDYATRLCTQFIAGEEAVTEDIQPFMSAMRAEGRLADEMYLTQFAFEEAKHTQVFRMWLDAVGISEDLHRYLDDLPAYRQIFYAELPECLNALSADPSPAAQVRASVTYNHIVEGMLALTGYYAWHKICVERAILPGMQELVRRIGDDERRHMAWGTFTCRRHVAADDANWTVFETRMNELIPLALRLIEEGFALYGDQPPFDLSKDDFLQYSTDKGMRRFGTISNARGRPVAEIDV 290
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.......hhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ee4 A   2 TRTRSGSLAAGGLNWASLPLKLFAGGNAKFWHPADIDFTRDRADWEKLSDDERDYATRLCTQFIAGEEAVTEDIQPFMSAMRAEGRLADEMYLTQFAFEEAKHTQVFRMWLDAVGISEDLHRYLDDLPAYRQIFYAELPECLNALSADPSPAAQVRASVTYNHIVEGMLALTGYYAWHKICVERAILPGMQELVRRIGDDERRHMAWGTFTCRRHVAADDANWTVFETRMNELIPLALRLIEEGFALYGDQPPFDLSKDDFLQYSTDKGMRRFGTISNARGRPVAEIDV 290
                                    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         


Chain A from PDB  Type:PROTEIN  Length:289
 aligned with RIR2H_MYCTU | P9WH69 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:289
                                    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         
          RIR2H_MYCTU     2 TRTRSGSLAAGGLNWASLPLKLFAGGNAKFWHPADIDFTRDRADWEKLSDDERDYATRLCTQFIAGEEAVTEDIQPFMSAMRAEGRLADEMYLTQFAFEEAKHTQVFRMWLDAVGISEDLHRYLDDLPAYRQIFYAELPECLNALSADPSPAAQVRASVTYNHIVEGMLALTGYYAWHKICVERAILPGMQELVRRIGDDERRHMAWGTFTCRRHVAADDANWTVFETRMNELIPLALRLIEEGFALYGDQPPFDLSKDDFLQYSTDKGMRRFGTISNARGRPVAEIDV 290
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.......hhhhhhhhhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ee4 A   2 TRTRSGSLAAGGLNWASLPLKLFAGGNAKFWHPADIDFTRDRADWEKLSDDERDYATRLCTQFIAGEEAVTEDIQPFMSAMRAEGRLADEMYLTQFAFEEAKHTQVFRMWLDAVGISEDLHRYLDDLPAYRQIFYAELPECLNALSADPSPAAQVRASVTYNHIVEGMLALTGYYAWHKICVERAILPGMQELVRRIGDDERRHMAWGTFTCRRHVAADDANWTVFETRMNELIPLALRLIEEGFALYGDQPPFDLSKDDFLQYSTDKGMRRFGTISNARGRPVAEIDV 290
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 3EE4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EE4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EE4)

(-) Gene Ontology  (11, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (RIR2H_MYCTO | P9WH68)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0009186    deoxyribonucleoside diphosphate metabolic process    The chemical reactions and pathways involving a deoxyribonucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with diphosphate on the sugar.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Chain A   (RIR2H_MYCTU | P9WH69)
molecular function
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) 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: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: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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        RIR2H_MYCTO | P9WH68: 4ac8
        RIR2H_MYCTU | P9WH69: 4ac8

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