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(-) Description

Title :  STRUCTURE OF COBALAMIN-DEPENDENT S-ADENOSYLMETHIONINE RADICAL ENZYME OXSB WITH AQUA-COBALAMIN 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 :  1.80
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, 28)

Asymmetric/Biological Unit (5, 28)
No.NameCountTypeFull Name
1B121Ligand/IonCOBALAMIN
2DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3EDO24Ligand/Ion1,2-ETHANEDIOL
4MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:313 , SER A:316 , CYS A:318 , CYS A:321 , ARG A:399 , DTT A:803binding site for residue SF4 A 801
02AC2SOFTWAREPHE A:131 , ARG A:135 , SER A:139 , GLN A:161 , 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 , GLU A:545 , DTT A:803 , EDO A:821 , HOH A:904 , HOH A:924 , HOH A:987 , HOH A:1001 , HOH A:1009 , HOH A:1032 , HOH A:1036 , HOH A:1064 , HOH A:1088 , HOH A:1142 , HOH A:1226 , HOH A:1267 , HOH A:1326 , HOH A:1331 , HOH A:1396 , HOH A:1420binding site for residue B12 A 802
03AC3SOFTWAREGLU A:363 , ALA A:397 , SF4 A:801 , B12 A:802 , HOH A:1031 , HOH A:1064 , HOH A:1126binding site for residue DTT A 803
04AC4SOFTWARETRP A:88 , HIS A:89 , SER A:107 , CYS A:108 , ASP A:314 , ARG A:317 , GLU A:368 , PRO A:370 , HOH A:914 , HOH A:1321binding site for residue MES A 804
05AC5SOFTWAREASN A:468 , LEU A:469 , HOH A:948 , HOH A:1181binding site for residue EDO A 805
06AC6SOFTWARELEU A:469 , ARG A:470 , VAL A:537 , HOH A:942 , HOH A:969binding site for residue EDO A 806
07AC7SOFTWAREMET A:475 , LEU A:493 , TYR A:534 , MET A:540 , LEU A:541 , HIS A:638 , HOH A:1055binding site for residue EDO A 807
08AC8SOFTWARETYR A:539 , MET A:540 , ILE A:601 , EDO A:828 , HOH A:1078 , HOH A:1191binding site for residue EDO A 808
09AC9SOFTWAREVAL A:617 , THR A:714 , ASP A:715 , HOH A:1034binding site for residue EDO A 809
10AD1SOFTWAREASP A:703 , ALA A:706 , ASP A:707 , LYS A:710binding site for residue EDO A 810
11AD2SOFTWARELYS A:257 , LEU A:258 , ASP A:259 , GLU A:269 , HOH A:922 , HOH A:1204binding site for residue EDO A 811
12AD3SOFTWAREASP A:259 , ASN A:276 , HOH A:1253binding site for residue EDO A 812
13AD4SOFTWAREGLU A:150 , HOH A:1344binding site for residue EDO A 813
14AD5SOFTWAREPRO A:75 , HOH A:1063binding site for residue EDO A 814
15AD6SOFTWARETHR A:373 , GLN A:376 , ARG A:377 , ASP A:380binding site for residue EDO A 815
16AD7SOFTWARESER A:6 , SER A:9 , GLU A:44 , LYS A:588 , THR A:589 , GLY A:681 , HOH A:1358binding site for residue EDO A 816
17AD8SOFTWAREMET A:251 , ASN A:619binding site for residue EDO A 817
18AD9SOFTWARELEU A:327 , ARG A:328 , SER A:329 , HOH A:932binding site for residue EDO A 818
19AE1SOFTWARETYR A:627 , ARG A:634 , HOH A:1046 , HOH A:1163binding site for residue EDO A 819
20AE2SOFTWARETYR A:201 , ARG A:230 , TYR A:231 , PRO A:232 , SER A:233binding site for residue EDO A 820
21AE3SOFTWAREARG A:135 , TYR A:359 , B12 A:802 , HOH A:1058 , HOH A:1170binding site for residue EDO A 821
22AE4SOFTWAREILE A:24 , ASP A:344 , ARG A:347 , HOH A:901 , HOH A:1167binding site for residue EDO A 822
23AE5SOFTWAREPHE A:432 , GLU A:436 , GLY A:472 , HOH A:1126binding site for residue EDO A 823
24AE6SOFTWAREGLU A:545 , HOH A:924 , HOH A:1061 , HOH A:1382binding site for residue EDO A 824
25AE7SOFTWAREGLU A:94 , ILE A:95 , GLU A:96 , LYS A:239 , ASP A:324 , EDO A:826binding site for residue EDO A 825
26AE8SOFTWARESER A:221 , PHE A:222 , ASP A:238 , ASP A:324 , EDO A:825 , HOH A:977binding site for residue EDO A 826
27AE9SOFTWAREHIS A:665 , LYS A:699 , LEU A:700 , ASP A:703binding site for residue EDO A 827
28AF1SOFTWARESER A:538 , MET A:540 , ARG A:634 , EDO A:808 , HOH A:1078 , HOH A:1176binding site for residue EDO A 828

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5UL3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5UL3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5UL3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UL3)

(-) Exons   (0, 0)

(no "Exon" information available for 5UL3)

(-) 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:727
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh........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.....eee.eehhhhh.....hhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhh....hhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh...hhhhhh........ee..hhhhhhhhhhhhhhh....hhhhh......ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ul3 A   6 STKSIEYYLKELKEIFSQIWLKPSEIEKRCEELFKRSKEFDYKRILVSGETDNTTLYVIEDSSKIHVFSPNRDLRENPLLMRWHPSWYEIESKEIYYKCFLSCEELYEHLELPTVTLVNLCVIENFPIPRLNLSTGTLSSYLRKEQLAKVELIDMQVGTTINQIIKNLLDSQPDIIGLSVNFGQKKLAFEILDLIYSHIENGDLSSIITVGNVIPSFSPEQFFERYPSLLICDKEGEYTLRDLIKMLKKELKLDEVNGISYVDESGEVKHNVAETVNFKEEVPTPSLDILGEISKFRGALTLETSRGCDYSRCTFCPRDHKLRSWRPLSVEQTLKQLDDILRAGKHFNIKPHIYMADEEFIGELPNGTEAQRIIDICEGLLKREEKIKFDFAARADSVYEPKRTKEWNVERLKMWHYCALAGADRIFIGVESGSNQQLKRYGKGTTSEQNIIALRLVSALGINLRIGFIMFDQLMKGLDNLKENLDFLERTDALMKPIDIGDMTYEELYDKLLNDKEFIEKHKTGKPVYTIVSYMLASMEILMNTPYSRMVQLTERKEEVNLIMNDGKPDMNMGRYATSFVDKTNGNLSEACQMWIDSNFGVMYTIKSLHKVANPREKKKLYSYMETHREISHFLLKYLVYNLSPDKESQIILSDFLRMHSMEHIKINVGDGSKENILNVMTNWQLIMEKLLRDVEADLNKGIITDSEDHRLHNTLKRWFSDMGNWS 736
                                    15        25        35        45        55        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       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665    || 679       689       699       709       719       729       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  670|                                                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   675
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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 5UL3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UL3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UL3)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/TrEMBL
        O24770_BACME | O24770: 5ul2 5ul4

(-) Related Entries Specified in the PDB File

5ul2 D_1000226059 D_1000226054
5ul4