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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM THERMOTOGA MARITIMA WITH GLYCEROL IN THE ACTIVE SITE
 
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) - 14 Jan 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
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 28199 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  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2ZN2Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:594 , HIS A:598 , CYS A:605 , CYS A:608BINDING SITE FOR RESIDUE ZN A 652
2AC2SOFTWARECYS B:594 , HIS B:598 , CYS B:605 , CYS B:608BINDING SITE FOR RESIDUE ZN B 652
3AC3SOFTWARETYR B:112 , HIS B:114 , ASP B:115 , GLU B:500 , LYS B:501 , ALA B:502 , HOH B:2033BINDING SITE FOR RESIDUE GOL B1641
4AC4SOFTWARETYR A:112 , HIS A:114 , ASP A:115 , ALA A:499 , GLU A:500 , LYS A:501 , ALA A:502 , HOH A:2053BINDING SITE FOR RESIDUE GOL A1640
5AC5SOFTWAREARG A:395 , ASP A:475 , THR A:476 , GLU A:479 , ASP B:471 , ASP B:475 , LYS B:549BINDING SITE FOR RESIDUE GOL A1641
6AC6SOFTWAREPRO B:606 , VAL B:607 , HOH B:2195BINDING SITE FOR RESIDUE GOL B1642
7AC7SOFTWAREGLN A:157 , HOH A:2082 , HOH A:2272 , GLN B:157BINDING SITE FOR RESIDUE GOL A1642

(-) SS Bonds  (0, 0)

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

(-) 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 4COI)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4COI)

(-) 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:606
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.hhhhh.....eee..hhhhhhhh.............hhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...........eeeeeehhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..ee.hhhhhhhhhhhhh....eeeeee............................eeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhh.eeeeeeeehhhhhhhhh..eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhh...eeeee..eee.....ee.............eeeee....eeehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4coi A   1 MKVQYSFEREFEELMSDLLSKYGYEMFQMDGLGDQLDVVKFTEDFVRVTNISTYFIEISKPHTYLYSLYRIWQKMKEMFGKGVADEFVEAQINGAVYLHDRHHAALMPYCFAYTLKPIVEKGLPFIKTIKSEPAKHLSTFIQHVIQFVMFASNQSSGAVGLPDFFVWMWYFVKKDLKEGIIPRDKLDWYIEQHFQILTYSLNQPIRTTQSPYTNFTYLDRNYIKAIFEGERYPDGSLITDHVEDIIALQKHYWEWVSRERERQMFTFPVLTASLLYKDGKFLDEDSARFINKINMKWQDTNWYISDSIDAVASCCREKLKGRMNSIGGSDLNIGSFKVITVNLPRIALESGGDREKYLQILRHRVQLIKKALAAVREIIKERISEGLLPLYENGLMLLNRQYGTIGVTGVWESASIMGLTTEDIDGLKYTEEGEVFVDNVLDTIREEAEKGYHEYGFTFNIEQVPAEKAAVTLAQKDRFLFGEKQPFEIYSNQWVPLMANTDVLNRIRYSGKWDKKVSGGAILHINLGESFKTEEESFNMVKMIADMGVMYFAFNTKISVCEDGHAFYGERCPVCGKAKVDEYMRIVGYLVPVSAFNKERREIEYP 639
                                    10        20        30        40      ||65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325     ||353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633      
                                                                         47|                                                                                                                                                                                                                                                                         331|                                                                                                                                                                                                                                                                                                 
                                                                          63                                                                                                                                                                                                                                                                          350                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:611
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.hhhhh.....eee..hhhhhhhh.............hhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...........eeeeeehhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee..ee.hhhhhhhhhhhhh....eeeeee..hhhhh...................eeeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhh.eeeeeeeehhhhhhhhhh.eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhh...eeeee..eeee....ee...........eeeeeee....eeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4coi B   1 MKVQYSFEREFEELMSDLLSKYGYEMFQMDGLGDQLDVVKFTEDFVRRGIIESTIDVTNISTYFIEISKPHTYLYSLYRIWQKMKEMFGKGVADEFVEAQINGAVYLHDRHHAALMPYCFAYTLKPIVEKGLPFIKTIKSEPAKHLSTFIQHVIQFVMFASNQSSGAVGLPDFFVWMWYFVKKDLKEGIIPRDKLDWYIEQHFQILTYSLNQPIRTTQSPYTNFTYLDRNYIKAIFEGERYPDGSLITDHVEDIIALQKHYWEWVSRERERQMFTFPVLTASLLYKDGKFLDEDSARFINKINMKWQDTNWYISDSIDAVASCCEKLKGRMNSIGGSDLNIGSFKVITVNLPRIALESGGDREKYLQILRHRVQLIKKALAAVREIIKERISEGLLPLYENGLMLLNRQYGTIGVTGVWESASIMGLTTEDIDGLKYTEEGEVFVDNVLDTIREEAEKGYHEYGFTFNIEQVPAEKAAVTLAQKDRFLFGEKQPFEIYSNQWVPLMANTDVLNRIRYSGKWDKKVSGGAILHINLKTEEESFNMVKMIADMGVMYFAFNTKISVCEDGHAFYGERCPVCGKAKVDEYMRIVGYLVPVSAFNKERREIEYPR 640
                                    10        20        30        40        50     || 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       639 
                                                                                  56|                                                                                                                                                                                                                                                                        330|                                                                                                                                                                                                               560|                                                                           
                                                                                   63                                                                                                                                                                                                                                                                         350                                                                                                                                                                                                                565
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4COI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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UniProtKB/TrEMBL
        Q9WYL6_THEMA | Q9WYL6: 4coj 4col 4com 4con 4u3e

(-) Related Entries Specified in the PDB File

4coj CRYSTAL STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH DATP AND CTP
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