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(-) Description

Title :  CRYSTAL STRUCTURE OF S. AUREUS TARM G117R MUTANT IN COMPLEX WITH FONDAPARINUX, ALPHA-GLCNAC-GLYCEROL AND UDP
 
Authors :  L. J. Worrall, S. Sobhanifar, N. C. Strynadka
Date :  09 Dec 14  (Deposition) - 25 Feb 15  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycosyltransferase Gt-B Retaining Wall Teichoic Acid, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sobhanifar, L. J. Worrall, R. J. Gruninger, G. A. Wasney, M. Blaukopf, L. Baumann, E. Lameignere, M. Solomonson, E. D. Brown, S. G. Withers, N. C. Strynadka
Structure And Mechanism Of Staphylococcus Aureus Tarm, The Wall Teichoic Acid Alpha-Glycosyltransferase.
Proc. Natl. Acad. Sci. Usa V. 112 E576 2015
PubMed-ID: 25624472  |  Reference-DOI: 10.1073/PNAS.1418084112

(-) Compounds

Molecule 1 - TARM
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET41B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SA21178_0837
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS 21178
    Organism Taxid: 904724

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
13YW2Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL 2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSIDE
2NTO2Ligand/IonTRISULFOAMINO HEPARIN PENTASACCHARIDE
3UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
13YW1Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL 2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSIDE
2NTO1Ligand/IonTRISULFOAMINO HEPARIN PENTASACCHARIDE
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
13YW1Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL 2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSIDE
2NTO1Ligand/IonTRISULFOAMINO HEPARIN PENTASACCHARIDE
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:16 , GLY A:17 , SER A:20 , LYS A:59 , ILE A:324 , SER A:325 , ARG A:326 , LYS A:331 , GLY A:356 , TYR A:382 , THR A:383 , PRO A:386 , GLY A:406 , LEU A:407 , SER A:408 , GLU A:411 , 3YW A:503 , HOH A:615 , HOH A:630 , HOH A:669binding site for residue UDP A 501
2AC2SOFTWAREHIS A:9 , LYS A:15 , GLY A:16 , GLY A:17 , MET A:18 , THR A:19 , PHE A:41 , ARG A:62 , ARG A:63 , ASN A:185 , ASN A:202 , ASN A:203 , GLY A:229 , SER A:230 , LYS A:233 , ARG A:326 , 3YW A:503 , HOH A:603 , HOH A:607 , HOH A:611 , HOH A:614 , HOH A:618 , HOH A:622 , HOH A:629 , HOH A:631 , HOH A:632 , HOH A:644 , HOH A:674 , HOH A:683 , HOH A:689 , HOH A:693 , HOH A:725binding site for residue NTO A 502
3AC3SOFTWAREGLY A:17 , MET A:18 , HIS A:249 , VAL A:250 , LEU A:282 , ASN A:304 , ARG A:326 , TYR A:402 , GLU A:403 , GLY A:404 , GLN A:405 , GLY A:406 , LEU A:407 , UDP A:501 , NTO A:502 , HOH A:647binding site for residue 3YW A 503
4AC4SOFTWAREGLY B:16 , GLY B:17 , MET B:18 , SER B:20 , LYS B:59 , ILE B:324 , SER B:325 , ARG B:326 , LYS B:331 , GLY B:356 , TYR B:382 , THR B:383 , PRO B:386 , GLY B:406 , LEU B:407 , SER B:408 , GLU B:411 , 3YW B:503 , HOH B:612 , HOH B:631 , HOH B:705binding site for residue UDP B 501
5AC5SOFTWAREHIS B:9 , LYS B:15 , GLY B:16 , GLY B:17 , MET B:18 , THR B:19 , PHE B:41 , ARG B:63 , ASN B:202 , ASN B:203 , LEU B:204 , GLY B:229 , SER B:230 , LYS B:233 , ARG B:326 , 3YW B:503 , HOH B:604 , HOH B:606 , HOH B:613 , HOH B:614 , HOH B:621 , HOH B:634 , HOH B:641 , HOH B:660 , HOH B:672 , HOH B:692 , HOH B:703binding site for residue NTO B 502
6AC6SOFTWAREGLY B:17 , MET B:18 , HIS B:249 , VAL B:250 , LEU B:282 , ASN B:304 , ARG B:326 , TYR B:402 , GLU B:403 , GLY B:404 , GLN B:405 , GLY B:406 , UDP B:501 , NTO B:502 , HOH B:616binding site for residue 3YW B 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X7R)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:425 -Tyr A:426
2Lys B:425 -Tyr B:426

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X7R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X7R)

(-) Exons   (0, 0)

(no "Exon" information available for 4X7R)

(-) Sequences/Alignments

Asymmetric 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:493
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh........eeehhhhhhhhhhh.....hhhhhhhhhhhh..eeeee....eeeeee.....eeeeeeee..eeeeeeee..eeeeeeeee..eeeeeeee.....eeeeeee.....eeeeeee......eeeeee....eee.hhhhhhhhhhhhhh.....eeeee.hhhhhhhhhh......eeeee...............hhhhhhhhhhhhhh.eeee.hhhhhhhhhhhh....eee..................eeeee...hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh.....eeeee...hhhhhhhh..eeee.......hhhhhhhhhh...eeee....hhhhhh.....eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x7r A   1 MKKIFMMVHELDVNKGGMTSSMFNRSKEFYDADIPADIVTFDYKGNYDEIIKALKKQGKMDRRTKMYNVFEYFKQISNNKHFKSNKLLYKHISERLKNTIEIEESKGISRYFDITTRTYIAYIRKSKSEKVIDFFKDNKRIERFSFIDNKVHMKETFNVDNKVCYQVFYDEKGYPYISRNINANNGAVGKTYVLVNKKEFKNNLALCVYYLEKLIKDSKDSIMICDGPGSFPKMFNTNHKNAQKYGVIHVNHHENFDDTGAFKKSEKYIIENANKINGVIVLTEAQRLDILNQFDVENIFTISNFVKIHNAPKHFQTEKIVGHISRMVPTKRIDLLIEVAELVVKKDNAVKFHIYGEGSVKDKIAKMIEDKNLERNVFLKGYTTTPQKCLEDFKLVVSTSQYEGQGLSMIEAMISKRPVVAFDIKYGPSDFIEDNKNGYLIENHNINDMADKILQLVNNDVLAAEFGSKARENIIEKYSTESILEKWLNLFNS 493
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490   


Chain B from PDB  Type:PROTEIN  Length:493
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh........eeehhhhhhhhhhh.....hhhhhhhhhhhh..eeeee....eeeeee.....eeeeeeee..eeeeeeee..eeeeeeeee..eeeeeeee.....eeeeeee.....eeeeeee......eeeeee....eee.hhhhhhhhhhhhhh.....eeeee.hhhhhhhhhh......eeeee...............hhhhhhhhhhhhhh.eeee.hhhhhhhhhhhh....eee..................eeeee...hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh.....eeeee...hhhhhhhh..eeee.......hhhhhhhhhh...eeee....hhhhhh.....eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x7r B   1 MKKIFMMVHELDVNKGGMTSSMFNRSKEFYDADIPADIVTFDYKGNYDEIIKALKKQGKMDRRTKMYNVFEYFKQISNNKHFKSNKLLYKHISERLKNTIEIEESKGISRYFDITTRTYIAYIRKSKSEKVIDFFKDNKRIERFSFIDNKVHMKETFNVDNKVCYQVFYDEKGYPYISRNINANNGAVGKTYVLVNKKEFKNNLALCVYYLEKLIKDSKDSIMICDGPGSFPKMFNTNHKNAQKYGVIHVNHHENFDDTGAFKKSEKYIIENANKINGVIVLTEAQRLDILNQFDVENIFTISNFVKIHNAPKHFQTEKIVGHISRMVPTKRIDLLIEVAELVVKKDNAVKFHIYGEGSVKDKIAKMIEDKNLERNVFLKGYTTTPQKCLEDFKLVVSTSQYEGQGLSMIEAMISKRPVVAFDIKYGPSDFIEDNKNGYLIENHNINDMADKILQLVNNDVLAAEFGSKARENIIEKYSTESILEKWLNLFNS 493
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490
   Legend:   → Mismatch (orange background)
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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 4X7R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X7R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X7R)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4X7R)

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        A0A0J9X256_S | A0A0J9X256: 4x7m

(-) Related Entries Specified in the PDB File

4x6l 4x7m 4x7p