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(-) Description

Title :  CRYSTAL STRUCTURE OF STEPTOCOCCUS PNEUMONIAE UNDECAPRENYL PYROPHOSPHATE SYNTHASE (UPPS) WITH FARNESYL DIPHOSPHATE
 
Authors :  N. O. Concha
Date :  14 Jun 16  (Deposition) - 20 Jul 16  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Upps, Native, Bacterial, Undecaprenyl S. Pneumoniae, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Concha, J. Huang, X. Bai, A. Benowitz, P. Brady, L. C. Grady, L. H. Kryn, D. Holmes, K. Ingraham, Q. Jin, L. Pothier Kaushansky, L. Mccloskey, J. A. Messer, H. O'Keefe, A. Patel, A. L. Satz, R. H. Sinnamon, J. Schneck, S. R. Skinner, J. Summerfield, A. Taylor, J. D. Taylor, G. Evindar, R. A. Stavenger
Discovery And Characterization Of A Class Of Pyrazole Inhibitors Of Bacterial Undecaprenyl Pyrophosphate Synthase
J. Med. Chem. V. 59 7299 2016
PubMed-ID: 27379833  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00746

(-) Compounds

Molecule 1 - ISOPRENYL TRANSFERASE
    Chains: A, B
    EC Number: 2.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UPPS, SP_0261
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE SEROTYPE 4 (STRAIN ATCC BAA-334 / TIGR4)
    Organism Taxid: 170187
    Strain: ATCC BAA-334 / TIGR4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FPP2Ligand/IonFARNESYL DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:28 , GLY A:29 , ASN A:30 , GLY A:31 , HIS A:45 , ALA A:71 , ARG A:79 , LEU A:90 , PHE A:143 , ARG A:206binding site for residue FPP A 301
2AC2SOFTWAREMET B:27 , ASP B:28 , GLY B:29 , ASN B:30 , GLY B:31 , ARG B:32 , HIS B:45 , MET B:49 , ALA B:71 , ARG B:79 , LEU B:90 , PHE B:143 , LEU B:145binding site for residue FPP B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KH4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val B:15 -Pro B:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KH4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KH4)

(-) Exons   (0, 0)

(no "Exon" information available for 5KH4)

(-) 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:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...eeee............hhhhhheeee...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kh4 A  14 EVPTQVPAHIGIIMDGNGRWAKKRMQPRVFGHKAGMEALQTVTKAANKLGVKVITVYAFSTENWTRPDQEVKFIMNLPVEFYDNYVPELHANNVKIQMIGETDRLPKQTFEALTKAEELTKNNTGLILNFALNYGGRAEITQALKLISQDVLDAKINPGDITEELIGNYLFTQHLPKDLRDPDLIIRTSGELRLSNFLPWQGAYSELYFTDTLWPDFDEAALQEAILAYNR 244
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243 


Chain B from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...eeee..................eeee...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kh4 B  15 VPTQVPAHIGIIMDGNGRWAKKRMQPRVFGHKAGMEALQTVTKAANKLGVKVITVYAFSTENWTRPDQEVKFIMNLPVEFYDNYVPELHANNVKIQMIGETDRLPKQTFEALTKAEELTKNNTGLILNFALNYGGRAEITQALKLISQDVLDAKINPGDITEELIGNYLFTQHLPKDLRDPDLIIRTSGELRLSNFLPWQGAYSELYFTDTLWPDFDEAALQEAILAYNR 244
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244
   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 5KH4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KH4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KH4)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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        ISPT_STRPN | Q97SR4: 5kh2 5kh5

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