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(-) Description

Title :  STRUCTURE OF COBALAMIN-DEPENDENT S-ADENOSYLMETHIONINE RADICAL ENZYME OXSB WITH AQUA-COBALAMIN AND S-ADENOSYLMETHIONINE BOUND
 
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 :  1.85
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 Taxid: 562
    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  (5, 19)

Asymmetric/Biological Unit (5, 19)
No.NameCountTypeFull Name
1B121Ligand/IonCOBALAMIN
2EDO15Ligand/Ion1,2-ETHANEDIOL
3MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4SAM1Ligand/IonS-ADENOSYLMETHIONINE
5SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:313 , SER A:316 , CYS A:318 , CYS A:321 , ARG A:399 , SAM A:803binding site for residue SF4 A 801
02AC2SOFTWAREPHE A:131 , ARG A:135 , SER A:139 , GLY A:182 , LEU A:183 , SER A:184 , PHE A:187 , GLY A:216 , ASN A:217 , CYS A:237 , LYS A:239 , GLU A:240 , GLY A:241 , GLU A:242 , GLU A:308 , ARG A:311 , CYS A:321 , PRO A:322 , HIS A:325 , LYS A:326 , ALA A:361 , GLU A:363 , SAM A:803 , EDO A:819 , HOH A:912 , HOH A:974 , HOH A:1008 , HOH A:1017 , HOH A:1053 , HOH A:1065 , HOH A:1084 , HOH A:1101 , HOH A:1146 , HOH A:1178 , HOH A:1269 , HOH A:1306binding site for residue B12 A 802
03AC3SOFTWAREPHE A:320 , GLU A:363 , ALA A:397 , ALA A:398 , ARG A:399 , PHE A:432 , GLY A:434 , GLU A:436 , LYS A:448 , GLY A:472 , PHE A:473 , ILE A:474 , SER A:543 , MET A:544 , GLU A:545 , SF4 A:801 , B12 A:802 , HOH A:906 , HOH A:912 , HOH A:924 , HOH A:952 , HOH A:986 , HOH A:1033 , HOH A:1082 , HOH A:1101 , HOH A:1241 , HOH A:1379binding site for residue SAM A 803
04AC4SOFTWARETRP A:88 , HIS A:89 , SER A:107 , CYS A:108 , ASP A:314 , ARG A:317 , GLU A:368 , LEU A:369 , PRO A:370 , EDO A:806 , HOH A:905 , HOH A:1035binding site for residue MES A 804
05AC5SOFTWARELEU A:14 , LYS A:18 , PRO A:75binding site for residue EDO A 805
06AC6SOFTWARETRP A:92 , MES A:804binding site for residue EDO A 806
07AC7SOFTWARETHR A:280 , LEU A:327 , ARG A:328 , SER A:329binding site for residue EDO A 807
08AC8SOFTWARETYR A:627 , MET A:630 , ARG A:634 , HOH A:963 , HOH A:1048binding site for residue EDO A 808
09AC9SOFTWAREARG A:430 , LEU A:469 , ARG A:470 , HOH A:1012binding site for residue EDO A 809
10AD1SOFTWAREASN A:468 , LEU A:469 , HOH A:994 , HOH A:1003binding site for residue EDO A 810
11AD2SOFTWAREGLU A:285 , SER A:334 , GLN A:337 , HOH A:1051binding site for residue EDO A 811
12AD3SOFTWARESER A:538 , TYR A:539 , MET A:540 , ARG A:634 , HOH A:930 , HOH A:943 , HOH A:1107 , HOH A:1120binding site for residue EDO A 812
13AD4SOFTWAREHIS A:351binding site for residue EDO A 813
14AD5SOFTWARELEU A:493 , TYR A:534 , MET A:540 , LEU A:541 , HIS A:638 , HOH A:981binding site for residue EDO A 814
15AD6SOFTWAREGLU A:116 , LYS A:625 , SER A:628 , HOH A:971binding site for residue EDO A 815
16AD7SOFTWAREARG A:135 , TYR A:359 , HOH A:907 , HOH A:1089 , HOH A:1100binding site for residue EDO A 816
17AD8SOFTWARELYS A:393 , ALA A:424binding site for residue EDO A 817
18AD9SOFTWAREHIS A:114 , LYS A:253 , GLU A:255 , HOH A:1169binding site for residue EDO A 818
19AE1SOFTWARETYR A:539 , B12 A:802binding site for residue EDO A 819

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5UL4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5UL4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5UL4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UL4)

(-) Exons   (0, 0)

(no "Exon" information available for 5UL4)

(-) 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:729
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.....eeeee.hhhhheeeeeee..eeeee....hhhhhhhhhhhh............eeeee.hhhhhhhhh..eeeeee............hhhhhhhhhhhhhh...eeeeee.hhh.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhh...eee...hhhhhhhhhhhhh...hhhhh..eeee.....eee......hhhhhh......hhhhhhhh...eee..ee...................ee.hhhhhhhhhhhhhhhhhhh....eeee............hhhhhhhhhhhhhhh.....eeeeeehhhhh.....hhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhh....hhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh...hhhhhh........ee..hhhhhhhhhhhhhh.....hhhhh......ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ul4 A   5 LSTKSIEYYLKELKEIFSQIWLKPSEIEKRCEELFKRSKEFDYKRILVSGETDNTTLYVIEDSSKIHVFSPNRDLRENPLLMRWHPSWYEIESKEIYYKCFLSCEELYEHLELPTVTLVNLCVIENFPIPRLNLSTGTLSSYLRKEQLAKVELIDMQVGTTINQIIKNLLDSQPDIIGLSVNFGQKKLAFEILDLIYSHIENGDLSSIITVGNVIPSFSPEQFFERYPSLLICDKEGEYTLRDLIKMLKKELKLDEVNGISYVDESGEVKHNVAETVNFKEEVPTPSLDILGEISKFRGALTLETSRGCDYSRCTFCPRDHKLRSWRPLSVEQTLKQLDDILRAGKHFNIKPHIYMADEEFIGELPNGTEAQRIIDICEGLLKREEKIKFDFAARADSVYEPKRTKEWNVERLKMWHYCALAGADRIFIGVESGSNQQLKRYGKGTTSEQNIIALRLVSALGINLRIGFIMFDQLMKGLDNLKENLDFLERTDALMKPIDIGDMTYEELYDKLLNDKEFIEKHKTGKPVYTIVSYMLASMEILMNTPYSRMVQLTERKEEVNLIMNDGKPDMNMGRYATSFVDKTNGNLSEACQMWIDSNFGVMYTIKSLHKVANPREKKKLYSYMETHREISHFLLKYLVYNLSPDKESQIILSDFLRMHSMEHILDNVGDGSKENILNVMTNWQLIMEKLLRDVEADLNKGIITDSEDHRLHNTLKRWFSDMGNWSL 737
                                    14        24        34        44        54        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       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       678       688       698       708       718       728         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     672|                                                            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      677
   Legend:   → Mismatch (orange background)
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    → 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 5UL4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UL4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UL4)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        O24770_BACME | O24770: 5ul2 5ul3

(-) Related Entries Specified in the PDB File

5ul2 D_1000226058 D_1000226054
5ul3