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(-) Description

Title :  ANAEROBIC RIBONUCLEOTIDE REDUCTASE
 
Authors :  M. A. Funk, C. L. Drennan
Date :  20 Jul 14  (Deposition) - 03 Sep 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Proteolysis, Barrel, Reductase, Radical, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Wei, M. A. Funk, L. A. Rosado, J. Baek, C. L. Drennan, J. Stubbe
The Class Iii Ribonucleotide Reductase From Neisseria Bacilliformis Can Utilize Thioredoxin As A Reductant.
Proc. Natl. Acad. Sci. Usa V. 111 E3756 2014
PubMed-ID: 25157154  |  Reference-DOI: 10.1073/PNAS.1414396111

(-) Compounds

Molecule 1 - RIBONUCLEOSIDE TRIPHOSPHATE REDUCTASE
    Chains: A, B
    EC Number: 1.17.4.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TM_0385, THEMA_02795, TMARI_0383
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: RIBONUCLEOTIDE REDUCTASE OF CLASS III (ANAEROBIC), LARGE SUBUNIT, UNCHARACTERIZED PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 48)

Asymmetric/Biological Unit (6, 48)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CIT2Ligand/IonCITRIC ACID
3GOL2Ligand/IonGLYCEROL
4MSE40Mod. Amino AcidSELENOMETHIONINE
5NA1Ligand/IonSODIUM ION
6ZN2Ligand/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 701
2AC2SOFTWARETYR A:112 , HIS A:114 , ASP A:115 , HIS A:117 , ALA A:499 , GLU A:500 , LYS A:501 , ALA A:502 , NA A:704 , ACT A:705 , HOH A:887 , HOH A:977 , HOH A:1150 , HOH A:1153binding site for residue CIT A 702
3AC3SOFTWARESER A:146 , GLU A:147 , THR A:154 , GLN A:157 , HIS A:158 , HOH A:941 , HOH A:986 , HOH A:1163 , TYR B:214 , GLN B:218binding site for residue GOL A 703
4AC4SOFTWAREASP A:115 , CIT A:702 , ACT A:705 , HOH A:1009binding site for residue NA A 704
5AC5SOFTWAREHIS A:114 , ASP A:115 , TYR A:124 , CIT A:702 , NA A:704 , HOH A:968binding site for residue ACT A 705
6AC6SOFTWARECYS B:594 , HIS B:598 , CYS B:605 , CYS B:608binding site for residue ZN B 901
7AC7SOFTWARETYR 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:1084 , HOH B:1116 , HOH B:1295 , HOH B:1355 , HOH B:1359binding site for residue CIT B 902
8AC8SOFTWARETYR A:214 , GLN A:218 , HOH A:1129 , GLU B:147 , GLN B:157 , HIS B:158 , HOH B:1172 , HOH B:1290binding site for residue GOL B 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U3E)

(-) 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 4U3E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U3E)

(-) Exons   (0, 0)

(no "Exon" information available for 4U3E)

(-) 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:637
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eee...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.hhhhh.....eee..hhhhhhhh.............hhhhhhhhhhhhhhhhh......eee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...........eeeeeehhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee..ee.hhhhhhhhhhhh.....eeeeee..hhhhh..................eeeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhh.eeeeeeeehhhhhhhhh..eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhh...eeeee..eeee....ee...........eeeeeee....eeehhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u3e A  -8 SGLVGSHmKVQYSFEREFEELmSDLLSKYGYEmFQmDGLGDQLDVVKFTEDFVRRGIIESTIDANANVRVTNISTYFIEISKPHTYLYSLYRIWQKmKEmFGKGVADEFVEAQINGAVYLHDRHHAALmPYCFAYTLKPIVEKGLPFIKTIKSEPAKHLSTFIQHVIQFVmFASNQSSGAVGLPDFFVWmWYFVKKDLKEGIIPRDKLDWYIEQHFQILTYSLNQPIRTTQSPYTNFTYLDRNYIKAIFEGERYPDGSLITDHVEDIIALQKHYWEWVSRERERQmFTFPVLTASLLYKDGKFLDEDSARFINKINmKWQDTNWYISDSIDAVASCEKLKGRmNSIGGSDLNIGSFKVITVNLPRIALESGGDREKYLQILRHRVQLIKKALAAVREIIKERISEGLLPLYENGLmLLNRQYGTIGVTGVWESASImGLTTEDIDGLKYTEEGEVFVDNVLDTIREEAEKGYHEYGFTFNIEQVPAEKAAVTLAQKDRFLFGEKQPFEIYSNQWVPLmANTDVLNRIRYSGKWDKKVSGGAILHINLGESFKTEEESFNmVKmIADmGVmYFAFNTKISVCEDGHAFYGERCPVCGKAKVDEYmRIVGYLVPVSAFNKERREIEYPRRQFYDSLTIR 650
                               ||  | 3        13 |      23  |  |  33        43        53        63        73        83      | 93       103       113       123       133       143       153       163|      173       183       193       203       213       223       233       243       253       263       273     | 283       293       303      |313       323     ||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       643       
                              -5|  |            15-MSE     26-MSE                                                          90-MSE                         122-MSE                                   164-MSE            183-MSE                                                                                         279-MSE                        310-MSE            329|     |                                                                      429-MSE              450-MSE                                                                          531-MSE                                   573-MSE  |  |                               617-MSE                             
                               -2  |                          29-MSE                                                          93-MSE                                                                                                                                                                                                                                      350     |                                                                                                                                                                                                                         576-MSE  |                                                                   
                                   1-MSE                                                                                                                                                                                                                                                                                                                                        356-MSE                                                                                                                                                                                                                         580-MSE                                                                  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   583-MSE                                                               


Chain B from PDB  Type:PROTEIN  Length:619
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...ee...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.hhhhh.....eee..hhhhhhhh.............hhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...........eeeeeehhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee..ee.hhhhhhhhhhhhh....eeeeee......................eeeeeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhh.eeeeeeeehhhhhhhhh..eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhh..eeeee..eee.....ee.............eeeee....eee.hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u3e B  -9 SSGLVmKVQYSFEREFEELmSDLLSKYGYEmFQmDGLGDQLDVVKFTEDFVRRGIIESTNISTYFIEISKPHTYLYSLYRIWQKmKEmFGKGVADEFVEAQINGAVYLHDRHHAALmPYCFAYTLKPIVEKGLPFIKTIKSEPAKHLSTFIQHVIQFVmFASNQSSGAVGLPDFFVWmWYFVKKDLKEGIIPRDKLDWYIEQHFQILTYSLNQPIRTTQSPYTNFTYLDRNYIKAIFEGERYPDGSLITDHVEDIIALQKHYWEWVSRERERQmFTFPVLTASLLYKDGKFLDEDSARFINKINmKWQDTNWYISDSIDAVAKLKGRmNSIGGSDLNIGSFKVITVNLPRIALESGGDREKYLQILRHRVQLIKKALAAVREIIKERISEGLLPLYENGLmLLNRQYGTIGVTGVWESASImGLTTEDIDGLKYTEEGEVFVDNVLDTIREEAEKGYHEYGFTFNIEQVPAEKAAVTLAQKDRFLFGEKQPFEIYSNQWVPLmANTDVLNRIRYSGKWDKKVSGGAILHINLGESFKTEEESFNmVKmIADmGVmYFAFNTKISVCEDGHAFYGERCPVCGKAKVDEYmRIVGYLVPVSAFNKERREIEYPRRQFYDSL 647
                                ||   5        15        25|  |    35        45       |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 ||    358       368       378       388       398       408       418       428|      438       448 |     458       468       478       488       498       508       518       528  |    538       548       558       568    |  578 |  |  588       598       608       618       628       638         
                               -5|            15-MSE     26-MSE                     53|                        90-MSE                         122-MSE                                   164-MSE            183-MSE                                                                                         279-MSE                        310-MSE          327|    |                                                                      429-MSE              450-MSE                                                                          531-MSE                                   573-MSE  |  |                               617-MSE                          
                                 1-MSE                      29-MSE                   64                           93-MSE                                                                                                                                                                                                                                    351    |                                                                                                                                                                                                                         576-MSE  |                                                                
                                                                                                                                                                                                                                                                                                                                                                 356-MSE                                                                                                                                                                                                                         580-MSE                                                               
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    583-MSE
   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 4U3E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U3E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U3E)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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        Q9WYL6_THEMA | Q9WYL6: 4coi 4coj 4col 4com 4con

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