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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH DATP AND CTP
 
Authors :  O. Aurelius, R. Johansson, V. Bagenholm, T. Beck, A. Balhuizen, D. Lund B. M. Sjoberg, E. Mulliez, D. T. Logan
Date :  28 Jan 14  (Deposition) - 06 May 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.48
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 01281 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
1CTP2Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
2DTP2Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
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 652
2AC2SOFTWARETYR A:112 , HIS A:114 , ASP A:115 , TYR A:124 , SER A:171 , ALA A:173 , ARG A:221 , GLN A:224 , TYR A:227 , SER A:358 , ILE A:359 , PRO A:498 , ALA A:499 , GLU A:500 , LYS A:501 , ALA A:502 , TYR A:622 , HOH A:2012 , HOH A:2013 , HOH A:2014 , HOH A:2015 , HOH A:2085BINDING SITE FOR RESIDUE CTP A 653
3AC3SOFTWARETRP A:203 , GLN A:207 , GLN A:210 , ILE A:211 , TYR A:214 , SER A:215 , GLN A:218 , MG A:655 , SER B:146 , GLU B:147 , ALA B:149 , LYS B:150 , HIS B:151 , THR B:154 , GLN B:157 , HIS B:158BINDING SITE FOR RESIDUE DTP A 654
4AC4SOFTWAREGLN A:207 , GLN A:210 , DTP A:654BINDING SITE FOR RESIDUE MG A 655
5AC5SOFTWARECYS B:594 , HIS B:598 , CYS B:605 , CYS B:608BINDING SITE FOR RESIDUE ZN B 652
6AC6SOFTWARETYR B:112 , HIS B:114 , ASP B:115 , TYR B:124 , SER B:171 , GLY B:172 , ALA B:173 , ARG B:221 , GLN B:224 , TYR B:227 , SER B:358 , ILE B:359 , PRO B:498 , ALA B:499 , GLU B:500 , LYS B:501 , ALA B:502 , TYR B:622 , HOH B:2007 , HOH B:2008 , HOH B:2009 , HOH B:2010 , HOH B:2011 , HOH B:2014 , HOH B:2077BINDING SITE FOR RESIDUE CTP B 653
7AC7SOFTWARESER A:146 , GLU A:147 , LYS A:150 , HIS A:151 , THR A:154 , GLN A:157 , HIS A:158 , GLN A:161 , TRP B:203 , GLN B:207 , GLN B:210 , ILE B:211 , TYR B:214 , SER B:215 , GLN B:218 , MG B:655 , HOH B:2035BINDING SITE FOR RESIDUE DTP B 654
8AC8SOFTWAREGLN B:207 , GLN B:210 , DTP B:654 , HOH B:2035BINDING SITE FOR RESIDUE MG B 655

(-) SS Bonds  (0, 0)

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

(-) 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 4COJ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4COJ)

(-) 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:594
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...........eee..hhhhhhhh.............hhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..........eeeeeehhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..ee.hhhhhhhhhhhhhhhh.eeeeee..hhhhh....................eeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhh.eeeeeeeehhhhhhhhh..eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhh..eeeee..eee.....ee.............eeeee....eeehhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4coj A   1 MKVQYSFEREFEELMSDLLSKYGYEMFQMDGLGDQLDVVKFTEDFVRTNISTYFIEISKPHTYLYSLYRIWQKMKEMFGKGVADEFVEAQINGAVYLHDRHHAALMPYCFAYTLKPIVEKGLPFIKTIKSEPAKHLSTFIQHVIQFVMFASNQSSGAVGLPDFFVWMWYFVKKDLKEGIIPRDKLDWYIEQHFQILTYSLNQPIRTTQSPYTNFTYLDRNYIKAIFEGERYPDGSLITDHVEDIIALQKHYWEWVSRERERQMFTFPVLTASLLYKDGKFLDEDSARFINKINMKWQDTNWYISDSIDAVASCCEKLKGRMNSIGGSDLNIGSFKVITVNLPRIALESGGDREKYLQILRHRVQLIKKALAAVREIIKERISEGLLPLYENGLMLLNRQYGTIGVTGVWESASIMGLTTEDIDGLKYTEEGEVFVDNVLDTIREEAEKGYHEYGFTFNIEQVPAEKAAVTLAQKDRFLFGEKQPFEIYSNQWVPLMANTDVLNRIRYSGKWDKKVSGGAILHINLKTEEESFNMVKMIADMGVMYFAFNTKISVCEDGHAFYGERCPVCGKAKVDEYMRIVGYLVPVSAFNKER 633
                                    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                                                                    


Chain B from PDB  Type:PROTEIN  Length:601
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...........eee..hhhhhhhh.............hhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...........eeeeeehhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh........eeeeeee.......hhhhhhhhhhhhhhhh.eeeeee..hhhhh...................eeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.......eeeeeeeehhhhhhhhhh.eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhhh...eeeee..eee.....ee.............eeeee....eeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4coj B   1 MKVQYSFEREFEELMSDLLSKYGYEMFQMDGLGDQLDVVKFTEDFVRRGTNISTYFIEISKPHTYLYSLYRIWQKMKEMFGKGVADEFVEAQINGAVYLHDRHHAALMPYCFAYTLKPIVEKGLPFIKTIKSEPAKHLSTFIQHVIQFVMFASNQSSGAVGLPDFFVWMWYFVKKDLKEGIIPRDKLDWYIEQHFQILTYSLNQPIRTTQSPYTNFTYLDRNYIKAIFEGERYPDGSLITDHVEDIIALQKHYWEWVSRERERQMFTFPVLTASLLYKDGKFLDEDSARFINKINMKWQDTNWYISDSIDAVASCEKLKGRMNSIGGSDLNIGSFKVITVNLPRIALESGGDREKYLQILRHRVQLIKKALAAVREIIKERISEGLLPLYENGLMLLNRQYGTIGVTGVWESASIMGLTTEDIDGLKYTEEGEVFVDNVLDTIREEAEKGYHEYGFTFNIEQVPAEKAAVTLAQKDRFLFGEKQPFEIYSNQWVPLMANTDVLNRIRYSGKWDKKVSGGAILHINLSFKTEEESFNMVKMIADMGVMYFAFNTKISVCEDGHAFYGERCPVCGKAKVDEYMRIVGYLVPVSAFNKERREIE 637
                                    10        20        30        40        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324    || 354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554     ||566       576       586       596       606       616       626       636 
                                                                           49|                                                                                                                                                                                                                                                                      329|                                                                                                                                                                                                               560|                                                                          
                                                                            64                                                                                                                                                                                                                                                                       350                                                                                                                                                                                                                563
   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 4COJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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UniProtKB/TrEMBL
        Q9WYL6_THEMA | Q9WYL6: 4coi 4col 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
4col CRYSTAL STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM THERMOTOGA MARITIMA WITH DATP BOUND IN THE SPECIFICITY SITE
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