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(-) Description

Title :  R2-LIKE LIGAND-BINDING OXIDASE WITH ANAEROBICALLY RECONSTITUTED DIIRON COFACTOR
 
Authors :  J. J. Griese, M. Hogbom
Date :  17 Dec 14  (Deposition) - 09 Sep 15  (Release) - 28 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  R2-Like Ligand-Binding Oxidase, Diiron Cofactor, Ribonucleotide Reductase R2 Subunit Fold, Metalloprotein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Griese, R. Kositzki, P. Schrapers, R. M. Branca, A. Nordstrom, J. Lehtio, M. Haumann, M. Hogbom
Structural Basis For Oxygen Activation At A Heterodinuclear Manganese/Iron Cofactor.
J. Biol. Chem. V. 290 25254 2015
PubMed-ID: 26324712  |  Reference-DOI: 10.1074/JBC.M115.675223

(-) Compounds

Molecule 1 - RIBONULEOTIDE REDUCTASE SMALL SUBUNIT
    Chains: A, B
    EC Number: 1.17.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-46 EK/LIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GK2771
    Organism Scientific: GEOBACILLUS KAUSTOPHILUS (STRAIN HTA426)
    Organism Taxid: 235909
    Synonym: R2-LIKE LIGAND-BINDING OXIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1FE26Ligand/IonFE (II) ION
2PLM2Ligand/IonPALMITIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:69 , GLU A:102 , HIS A:105 , GLU A:202 , FE2 A:402 , PLM A:404 , HOH A:546binding site for residue FE2 A 401
2AC2SOFTWAREGLU A:102 , GLU A:167 , GLU A:202 , HIS A:205 , FE2 A:401 , PLM A:404binding site for residue FE2 A 402
3AC3SOFTWAREHIS A:130 , HOH A:582 , HOH A:594 , HOH A:595binding site for residue FE2 A 403
4AC4SOFTWAREGLY A:64 , GLU A:69 , VAL A:72 , GLU A:102 , PHE A:135 , GLU A:167 , LEU A:170 , THR A:177 , GLU A:202 , TYR A:241 , FE2 A:401 , FE2 A:402 , HOH A:546binding site for residue PLM A 404
5AC5SOFTWAREGLU B:102 , GLU B:167 , GLU B:202 , HIS B:205 , FE2 B:402 , PLM B:404binding site for residue FE2 B 401
6AC6SOFTWAREGLU B:69 , GLU B:102 , HIS B:105 , GLU B:202 , FE2 B:401 , PLM B:404 , HOH B:599binding site for residue FE2 B 402
7AC7SOFTWAREHIS B:130 , HOH B:578 , HOH B:581 , HOH B:592binding site for residue FE2 B 403
8AC8SOFTWAREGLY B:64 , PHE B:65 , GLU B:69 , GLU B:102 , PHE B:135 , VAL B:166 , GLU B:167 , LEU B:170 , ALA B:171 , THR B:177 , GLU B:202 , FE2 B:401 , FE2 B:402 , HOH B:599binding site for residue PLM B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XBV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XBV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XBV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XBV)

(-) Exons   (0, 0)

(no "Exon" information available for 4XBV)

(-) 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:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.....hhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xbv A   2 VHHDGFQTVKATIDWEHPMFKLYEKAKRNGKWNPADIDFSQDQKDFASLTSEEKISALPLVAGFSAGEEAVTLDILPMAHALARQGRLEDVLFLTTFMHDEAKHVEMFSRWQQAVGIGQMDLSVFHNDHYKRIFYEALPEAMNRLYADDSPEAVIRAATVYNMIVEGTLAESGYYTFRQIYKKAGLFPGLLQGIDYLNMDEGRHIQFGIYTIQRIVNEDERYYELFIRYMDELWPHVIGYVDYLTELGKRQQQLARTYALEIDYDLLRHYVIKQFNLRKKQISRT 286
                                    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 B from PDB  Type:PROTEIN  Length:286
                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.....hhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xbv B   2 VHHDGFQTVKATIDWEHPMFKLYEKAKRNGKWNPADIDFSQDQKDFASLTSEEKISALPLVAGFSAGEEAVTLDILPMAHALARQGRLEDVLFLTTFMHDEAKHVEMFSRWQQAVGIGQMDLSVFHNDHYKRIFYEALPEAMNRLYADDSPEAVIRAATVYNMIVEGTLAESGYYTFRQIYKKAGLFPGLLQGIDYLNMDEGRHIQFGIYTIQRIVNEDERYYELFIRYMDELWPHVIGYVDYLTELGKRQQQLARTYALEIDYDLLRHYVIKQFNLRKKQISRTK 287
                                    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 4XBV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XBV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XBV)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  1.17.4.1
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 Related Entries

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

UniProtKB/TrEMBL
        Q5KW80_GEOKA | Q5KW80: 4hr0 4hr4 4hr5 4xb9 4xbw 5dco 5dcr 5dcs 5ekb

(-) Related Entries Specified in the PDB File

4hr0 4HR0 CONTAINS THE SAME PROTEIN WITH AEROBICALLY RECONSTITUTED MN/FE COFACTOR.
4hr4 4HR4 CONTAINS THE SAME PROTEIN WITH ANAEROBICALLY RECONSTITUTED MN/ FE COFACTOR.
4hr5 4HR5 CONTAINS THE SAME PROTEIN WITHOUT METAL COFACTOR.
4xb9 4XB9 CONTAINS THE SAME PROTEIN WITH AEROBICALLY RECONSTITUTED DIIRON COFACTOR.
4xbw 4XBW CONTAINS THE SAME PROTEIN WITH AEROBICALLY RECONSTITUTED DIMANGANESE COFACTOR