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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM THERMOTOGA MARITIMA WITH DATP BOUND IN THE SPECIFICITY SITE
 
Authors :  O. Aurelius, R. Johansson, V. Bagenholm, T. Beck, A. Balhuizen, D. Lund B. M. Sjoberg, E. Mulliez, D. T. Logan
Date :  29 Jan 14  (Deposition) - 06 May 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Radical Chemistry, Allosteric Regulation, Anaerobic Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Aurelius, R. Johansson, V. Bagenholm, T. Beck, A. Balhuizen, D. Lundin, B. M. Sjoberg, E. Mulliez, D. T. Logan
The Crystal Structure Of Thermotoga Maritima Class Iii Ribonucleotide Reductase Lacks A Radical Cysteine Pre- Positioned In The Active Site.
Plos One V. 10 01289 2015
PubMed-ID: 26147435  |  Reference-DOI: 10.1371/JOURNAL.PONE.0128199

(-) Compounds

Molecule 1 - ANAEROBIC RIBONUCLEOSIDE-TRIPHOSPHATE REDUCTASE
    Chains: A, B
    EC Number: 1.17.4.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: CODONPLUS-RIL
    Expression System Vector: PRSFDUET-1
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8
    Synonym: ANAEROBIC RIBONUCLEOTIDE REDUCTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1DTP2Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3SFO2Ligand/IonSULFONIC ACID
4ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:594 , HIS A:598 , CYS A:605 , CYS A:608BINDING SITE FOR RESIDUE ZN A 700
2AC2SOFTWAREGLN A:207 , GLN A:210 , DTP A:702 , HOH A:2069BINDING SITE FOR RESIDUE MG A 701
3AC3SOFTWARETRP A:203 , GLN A:207 , GLN A:210 , ILE A:211 , TYR A:214 , SER A:215 , MG A:701 , HOH A:2069 , HOH A:2071 , SER B:146 , GLU B:147 , ALA B:149 , LYS B:150 , HIS B:151 , THR B:154 , GLN B:157 , HIS B:158 , GLN B:161BINDING SITE FOR RESIDUE DTP A 702
4AC4SOFTWARECYS B:594 , HIS B:598 , CYS B:605 , CYS B:608BINDING SITE FOR RESIDUE ZN B 700
5AC5SOFTWAREGLN B:207 , GLN B:210 , DTP B:702 , HOH B:2050BINDING SITE FOR RESIDUE MG B 701
6AC6SOFTWARESER A:146 , GLU A:147 , ALA A:149 , LYS A:150 , HIS A:151 , THR A:154 , GLN A:157 , HIS A:158 , GLN A:161 , HOH A:2046 , TRP B:203 , GLN B:207 , GLN B:210 , ILE B:211 , TYR B:214 , SER B:215 , MG B:701 , HOH B:2050 , HOH B:2052BINDING SITE FOR RESIDUE DTP B 702
7AC7SOFTWARETYR A:112 , HIS A:114 , ASP A:115BINDING SITE FOR RESIDUE SFO A1631
8AC8SOFTWARETYR B:112 , HIS B:114 , ASP B:115 , LYS B:501BINDING SITE FOR RESIDUE SFO B1633

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:282 -Pro A:283
2Phe B:282 -Pro B:283

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4COL)

(-) 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:586
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...........eee..hhhhhhhh.............hhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...........eeeeeehhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee..ee.hhhhhhhhhhhh.....eeeeee..hhhhh.................eeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhh.eeeeeeeehhhhhhhhh..eee....eeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhh...eeeee..eee.....ee.............eeeee....eeehhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4col A   1 MKVQYSFEREFEELMSDLLSKYGYEMFQMDGLGDQLDVVKFTEDFVTNISTYFIEISKPHTYLYSLYRIWQKMKEMFGKGVADEFVEAQINGAVYLHDRHHAALMPYCFAYTLKPIVEKGLPFIKTIKSEPAKHLSTFIQHVIQFVMFASNQSSGAVGLPDFFVWMWYFVKKDLKEGIIPRDKLDWYIEQHFQILTYSLNQPIRTTQSPYTNFTYLDRNYIKAIFEGERYPDGSLITDHVEDIIALQKHYWEWVSRERERQMFTFPVLTASLLYKDGKFLDEDSARFINKINMKWQDTNWYISDSIDAVASKLKGRMNSIGGSDLNIGSFKVITVNLPRIALESGGDREKYLQILRHRVQLIKKALAAVREIIKERISEGLLPLYENGLMLLNRQYGTIGVTGVWESASIMGLTTEDIDGLKYTEEGEVFVDNVLDTIREEAEKGYHEYGFTFNIEQVPAEKAAVTLAQKDRFLFGEKQPFEIYSNQWVPLMANTDVLNRIRYSGKWDKKVSGGAILHINLTEEESFNMVKMIADMGVMYFAFNTKISVCEDGHAFYGERCPVCGKAKVDEYMRIVGYLVPVSAFN 630
                                    10        20        30        40     || 67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327||     359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559||     574       584       594       604       614       624      
                                                                        46|                                                                                                                                                                                                                                                                     328|                                                                                                                                                                                                              560|                                                                
                                                                         64                                                                                                                                                                                                                                                                      351                                                                                                                                                                                                               566                                                                


Chain B from PDB  Type:PROTEIN  Length:593
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.hhhhh.....eee..hhhhhhhh.............hhhhhhhhhhhhhhhhhh.....ee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..........eeeeeehhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee..ee.hhhhhhhhhhhh.....eeeeee..hhhhh...................eeeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhh.eeeeeeeehhhhhhhhh..eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhh...eeeee..eeee....ee...........eeeeeee....eeehhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4col B   1 MKVQYSFEREFEELMSDLLSKYGYEMFQMDGLGDQLDVVKFTEDFVRTNISTYFIEISKPHTYLYSLYRIWQKMKEMFGKGVADEFVEAQINGAVYLHDRHHAALMPYCFAYTLKPIVEKGLPFIKTIKSEPAKHLSTFIQHVIQFVMFASNQSSGAVGLPDFFVWMWYFVKKDLKEGIIPRDKLDWYIEQHFQILTYSLNQPIRTTQSPYTNFTYLDRNYIKAIFEGERYPDGSLITDHVEDIIALQKHYWEWVSRERERQMFTFPVLTASLLYKDGKFLDEDSARFINKINMKWQDTNWYISDSIDAVASCCEKLKGRMNSIGGSDLNIGSFKVITVNLPRIALESGGDREKYLQILRHRVQLIKKALAAVREIIKERISEGLLPLYENGLMLLNRQYGTIGVTGVWESASIMGLTTEDIDGLKYTEEGEVFVDNVLDTIREEAEKGYHEYGFTFNIEQVPAEKAAVTLAQKDRFLFGEKQPFEIYSNQWVPLMANTDVLNRIRYSGKWDKKVSGGAILHINLKTEEESFNMVKMIADMGVMYFAFNTKISVCEDGHAFYGERCPVCGKAKVDEYMRIVGYLVPVSAFNKE 632
                                    10        20        30        40      ||66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326   ||  355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555    || 569       579       589       599       609       619       629   
                                                                         47|                                                                                                                                                                                                                                                                       330|                                                                                                                                                                                                               560|                                                                   
                                                                          64                                                                                                                                                                                                                                                                        350                                                                                                                                                                                                                565
   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 4COL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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        Q9WYL6_THEMA | Q9WYL6: 4coi 4coj 4com 4con 4u3e

(-) Related Entries Specified in the PDB File

4coi CRYSTAL STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM THERMOTOGA MARITIMA WITH GLYCEROL IN THE ACTIVE SITE
4coj CRYSTAL STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH DATP AND CTP
4com CRYSTAL STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM THERMOTOGA MARITIMA WITH MES IN THE ACTIVE SITE
4con CRYSTAL STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM THERMOTOGA MARITIMA WITH CITRATE IN THE ACTIVE SITE