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(-) Description

Title :  STRUCTURE OF APO, SEMET-LABELED COBALAMIN-DEPENDENT S-ADENOSYLMETHIONINE RADICAL ENZYME OXSB
 
Authors :  J. Bridwell-Rabb, C. L. Drennan
Date :  24 Jan 17  (Deposition) - 19 Apr 17  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Metalloprotein, Cobalamin, Radical Sam, S-Adenosylmethionine, Oxetanocin, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Bridwell-Rabb, A. Zhong, H. G. Sun, C. L. Drennan, H. W. Liu
A B12-Dependent Radical Sam Enzyme Involved In Oxetanocin A Biosynthesis.
Nature V. 544 322 2017
PubMed-ID: 28346939  |  Reference-DOI: 10.1038/NATURE21689

(-) Compounds

Molecule 1 - OXSB PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 469008
    Gene: OXSB
    Organism Scientific: BACILLUS MEGATERIUM
    Organism Taxid: 1404

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 41)

Asymmetric/Biological Unit (2, 41)
No.NameCountTypeFull Name
1EDO17Ligand/Ion1,2-ETHANEDIOL
2MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMSE A:475 , LEU A:493 , TYR A:534 , MSE A:540 , LEU A:541 , HIS A:638 , HOH A:909binding site for residue EDO A 801
02AC2SOFTWAREPHE A:320 , ILE A:474 , GLU A:545binding site for residue EDO A 802
03AC3SOFTWAREGLU A:631 , ARG A:634binding site for residue EDO A 803
04AC4SOFTWAREILE A:467 , ASN A:468 , LEU A:469 , LEU A:499binding site for residue EDO A 804
05AC5SOFTWAREILE A:236 , GLY A:263 , SER A:265 , ASP A:324 , HOH A:932binding site for residue EDO A 805
06AC6SOFTWAREARG A:470 , THR A:535 , ILE A:536 , HOH A:924binding site for residue EDO A 806
07AC7SOFTWAREILE A:505 , MSE A:508 , TYR A:510 , EDO A:813binding site for residue EDO A 807
08AC8SOFTWAREALA A:618 , ASN A:619 , GLU A:622binding site for residue EDO A 808
09AC9SOFTWAREPHE A:222 , ASP A:324binding site for residue EDO A 809
10AD1SOFTWAREARG A:80 , SER A:97 , ARG A:554 , GLN A:557 , ARG A:561binding site for residue EDO A 810
11AD2SOFTWARETYR A:539binding site for residue EDO A 811
12AD3SOFTWAREGLU A:205 , ASN A:206 , GLY A:303 , HIS A:357binding site for residue EDO A 812
13AD4SOFTWARETHR A:509 , TYR A:510 , EDO A:807 , EDO A:817 , HOH A:934binding site for residue EDO A 813
14AD5SOFTWAREASN A:137 , LEU A:138 , THR A:140 , GLY A:141 , ASP A:159 , SER A:291 , ILE A:294binding site for residue EDO A 814
15AD6SOFTWAREGLY A:438 , SER A:439 , ASN A:440 , SER A:452 , GLU A:488binding site for residue EDO A 815
16AD7SOFTWAREPHE A:131 , PHE A:432 , ARG A:470 , SER A:538 , HOH A:902binding site for residue EDO A 816
17AD8SOFTWAREGLU A:415 , LYS A:418 , EDO A:813binding site for residue EDO A 817

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:318 -A:321

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:131 -Pro A:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5UL2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UL2)

(-) Exons   (0, 0)

(no "Exon" information available for 5UL2)

(-) 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:731
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh......eeeee.hhhhheeeeeee..eeeee....hhhhhhhhhhhh............eeeee.hhhhhhhh...eeeeeee.........ee..hhhhhhhhhhhh...eeeeee.hhh.hhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhh.....eee...hhhhhhhhhhhhh...hhhhh...eee.....eee......hhhhhh.....hhhhhh.....eeee..ee..hhhhh............ee.hhhhhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhh.....eeeeeehhhhh.....hhhhhhhhhhhhhhhhhhheeeeeeeee..hhhhhhhhh...hhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhh...hhhhhh............hhhhhhhhhhhhhhh....hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ul2 A   3 TYLSTKSIEYYLKELKEIFSQIWLKPSEIEKRCEELFKRSKEFDYKRILVSGETDNTTLYVIEDSSKIHVFSPNRDLRENPLLmRWHPSWYEIESKEIYYKCFLSCEELYEHLELPTVTLVNLCVIENFPIPRLNLSTGTLSSYLRKEQLAKVELIDmQVGTTINQIIKNLLDSQPDIIGLSVNFGQKKLAFEILDLIYSHIENGDLSSIITVGNVIPSFSPEQFFERYPSLLICDKEGEYTLRDLIKmLKKELKLDEVNGISYVDESGEVKHNVAETVNFKEEVPTPSLDILGEISKFRGALTLETSRGCDYSRCTFCPRDHKLRSWRPLSVEQTLKQLDDILRAGKHFNIKPHIYmADEEFIGELPNGTEAQRIIDICEGLLKREEKIKFDFAARADSVYEPKRTKEWNVERLKmWHYCALAGADRIFIGVESGSNQQLKRYGKGTTSEQNIIALRLVSALGINLRIGFImFDQLmKGLDNLKENLDFLERTDALmKPIDIGDmTYEELYDKLLNDKEFIEKHKTGKPVYTIVSYmLASmEILmNTPYSRmVQLTERKEEVNLImNDGKPDmNmGRYATSFVDKTNGNLSEACQmWIDSNFGVmYTIKSLHKVANPREKKKLYSYmETHREISHFLLKYLVYNLSPDKESQIILSDFLRmHSmEHIINVGDGSKENILNVmTNWQLImEKLLRDVEADLNKGIITDSEDHRLHNTLKRWFSDmGNWSLI 738
                                    12        22        32        42        52        62        72        82   |    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412      |422       432       442       452       462       472  |    482       492       502     | 512       522       532       542 |   | 552  |    562      |572   | | 582       592      |602     | 612       622       632       642       652       662 |  |  677       687  |    697       707       717       727    |  737 
                                                                                                              86-MSE                                                                   160-MSE                                                                                    251-MSE                                                                                                      360-MSE                                                    419-MSE                                                 475-MSE|                 500-MSE 508-MSE                         540-MSE   |      |           569-MSE  | |                  599-MSE  608-MSE               630-MSE                           664-MSE ||           690-MSE  |                                732-MSE  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       480-MSE                                                         544-MSE      |                  576-MSE                                                                                    667-MSE                  697-MSE                                     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           548-MSE  |                    578-MSE                                                                                     670|                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  555-MSE                                                                                                             676
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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 5UL2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UL2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UL2)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        O24770_BACME | O24770: 5ul3 5ul4

(-) Related Entries Specified in the PDB File

5ul3 D_1000226058 D_1000226059
5ul4