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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ANAEROBIC RIBONUCLEOTIDE REDUCTASE FROM THERMOTOGA MARITIMA WITH CITRATE 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 :  29 Jan 14  (Deposition) - 14 Jan 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
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  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:112 , HIS A:114 , ASP A:115 , HIS A:117 , ALA A:499 , GLU A:500 , LYS A:501 , ALA A:502 , HOH A:2014 , HOH A:2015 , HOH A:2080BINDING SITE FOR RESIDUE CIT A1589
2AC2SOFTWARETYR B:112 , HIS B:114 , ASP B:115 , HIS B:117 , ALA B:499 , GLU B:500 , LYS B:501 , ALA B:502 , HOH B:2010 , HOH B:2011 , HOH B:2087BINDING SITE FOR RESIDUE CIT B1590

(-) SS Bonds  (0, 0)

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

(-) 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 4CON)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CON)

(-) 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:543
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee...........eee..hhhhhhhh.............hhhhhhhhhhhhhhhhhhh....ee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh........eeeeeehhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee..ee.hhhhhhhhhhhh.....eeeeee..hhhhh................eeeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhh.eeeeeeeehhhhhhhhh..eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh....eee..hhhhhhhhhhhhhhh...eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4con A   1 MKVQYSFEREFEELMSDLLSKYGYEMFQMDGLGDQLDVVKFTEDFVRVTNISTYFIEISKPHTYLYSLYRIWQKMKEMFGKGVADEFVEAQINGAVYLHDRHHAALMPYCFAYTLKPIVEKGLPFIKTIKSEPAKHLSTFIQHVIQFVMFASNQSSGAVGLPDFFVWMWYFVKKDLKEGIIPRDKLDWYIEQHFQILTYSLNQPTQSPYTNFTYLDRNYIKAIFEGERYPDGSLITDHVEDIIALQKHYWEWVSRERERQMFTFPVLTASLLYKDGKFLDEDSARFINKINMKWQDTNWYISDSIDAVAEKLKGRMNSIGGSDLNIGSFKVITVNLPRIALESGGDREKYLQILRHRVQLIKKALAAVREIIKERISEGLLPLYENGLMLLNRQYGTIGVTGVWESASIMGLTTEDIDGLKYTEEGEVFVDNVLDTIREEAEKGYHEYGFTFNIEQVPAEKAAVTLAQKDRFLFGEKQPFEIYSNQWVPLMANTDVLNRIRYSGKWDKKVSGGAILHINKTEEESFNMVKMIADMGVMYFAFN 588
                                    10        20        30        40      ||65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215   ||  228       238       248       258       268       278       288       298       308       318       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       565       575       585   
                                                                         47|                                                                                                                                                         219|                                                                                                     327|                                                                                                                                                                                                              559|                       
                                                                          63                                                                                                                                                          223                                                                                                      350                                                                                                                                                                                                               565                       


Chain B from PDB  Type:PROTEIN  Length:553
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.hhhhh.....eee..hhhhhhhh.............hhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh........eeeeeehhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee..ee.hhhhhhhhhhhh.....eeeeee.........................eeeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhh.eeeeeeeehhhhhhhhh..eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhh...eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4con B   1 MKVQYSFEREFEELMSDLLSKYGYEMFQMDGLGDQLDVVKFTEDFVRRGIIESTIDTNISTYFIEISKPHTYLYSLYRIWQKMKEMFGKGVADEFVEAQINGAVYLHDRHHAALMPYCFAYTLKPIVEKGLPFIKTIKSEPAKHLSTFIQHVIQFVMFASNQSSGAVGLPDFFVWMWYFVKKDLKEGIIPRDKLDWYIEQHFQILTYSLNQPTQSPYTNFTYLDRNYIKAIFEGERYPDGSLITDHVEDIIALQKHYWEWVSRERERQMFTFPVLTASLLYKDGKFLDEDSARFINKINMKWQDTNWYISDSIDAVASCEKLKGRMNSIGGSDLNIGSFKVITVNLPRIALESGGDREKYLQILRHRVQLIKKALAAVREIIKERISEGLLPLYENGLMLLNRQYGTIGVTGVWESASIMGLTTEDIDGLKYTEEGEVFVDNVLDTIREEAEKGYHEYGFTFNIEQVPAEKAAVTLAQKDRFLFGEKQPFEIYSNQWVPLMANTDVLNRIRYSGKWDKKVSGGAILHINTEEESFNMVKMIADMGVMYFAFNT 589
                                    10        20        30        40        50     || 67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217 ||    230       240       250       260       270       280       290       300       310       320       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       566       576       586   
                                                                                  56|                                                                                                                                                        219|                                                                                                       329|                                                                                                                                                                                                              559|                       
                                                                                   64                                                                                                                                                         223                                                                                                        350                                                                                                                                                                                                               566
   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 4CON)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/TrEMBL
        Q9WYL6_THEMA | Q9WYL6: 4coi 4coj 4col 4com 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
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