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(-) Description

Title :  STRUCTURE OF B. ANTHRAX LETHAL FACTOR IN COMPLEX WITH A HYDROXAMATE INHIBITOR
 
Authors :  W. L. Shoop, Y. Xiong, J. Wiltsie, A. Woods, J. Guo, J. V. Pivnichny, T. Felcetto, B. F. Michael, A. Bansal
Date :  02 Feb 05  (Deposition) - 31 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Toxin, Lethal Factor, Inhibitors, Hydroxamate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. L. Shoop, Y. Xiong, J. Wiltsie, A. Woods, J. Guo, J. V. Pivnichny, T. Felcetto, B. F. Michael, A. Bansal, R. T. Cummings, B. R. Cunningham, A. M. Friedlander, C. M. Douglas, S. B. Patel, D. Wisniewski, G. Scapin, S. P. Salowe, D. M. Zaller, K. T. Chapman, E. M. Scolnick, D. M. Schmatz, K. Bartizal, M. Maccoss, J. D. Hermes
Anthrax Lethal Factor Inhibition.
Proc. Natl. Acad. Sci. Usa V. 102 7958 2005
PubMed-ID: 15911756  |  Reference-DOI: 10.1073/PNAS.0502159102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LETHAL FACTOR
    ChainsA
    EC Number3.4.24.83
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-4T-3
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentDOMAINS II-IV (RESIDUES 297-809)
    GeneLEF
    Organism ScientificBACILLUS ANTHRACIS
    Organism Taxid1392
    SynonymLF, ANTHRAX LETHAL TOXIN ENDOPEPTIDASE COMPONENT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
19151Ligand/Ion(2R)-2-{[(4-FLUORO-3-METHYLPHENYL)SULFONYL]AMINO}-N-HYDROXY-2-TETRAHYDRO-2H-PYRAN-4-YLACETAMIDE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:686 , HIS A:690 , GLU A:735 , 915 A:782BINDING SITE FOR RESIDUE ZN A 781
2AC2SOFTWAREASP A:328 , SER A:655 , LYS A:656 , GLY A:657 , LEU A:658 , VAL A:675 , LEU A:677 , HIS A:686 , GLU A:687 , HIS A:690 , TYR A:728 , GLU A:735 , GLU A:739 , ZN A:781 , HOH A:793 , HOH A:878BINDING SITE FOR RESIDUE 915 A 782

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YQY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YQY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LEF_BACAN_001 *A299SLEF_BACAN  ---  ---AS266S
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.LEF_BACAN716-725  1A:683-692

(-) Exons   (0, 0)

(no "Exon" information available for 1YQY)

(-) 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:514
 aligned with LEF_BACAN | P15917 from UniProtKB/Swiss-Prot  Length:809

    Alignment length:514
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         809  
                                   307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807 |  
            LEF_BACAN   298 LARYEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPIEPKKDDIIHSLSQEEKELLKRIQIDSSDFLSTEEKEFLKKLQIDIRDSLSEEEKELLNRIQVDSSNPLSEKEKEFLKKLKLDIQPYDINQRLQDTGGLIDSPSINLDVRKQYKRDIQNIDALLHQSIGSTLYNKIYLYENMNINNLTATLGADLVDSTDNTKINRGIFNEFKKNFKYSISSNYMIVDINERPALDNERLKWRIQLSPDTRAGYLENGKLILQRNIGLEIKDVQIIKQSEKEYIRIDAKVVPKSKIDTKIQEAQLNINQEWNKALGLPKYTKLITFNVHNRYASNIVESAYLILNEWKNNIQSDLIKKVTNYLVDGNGRFVFTDITLPNIAEQYTHQDEIYEQVHSKGLYVPESRSILLHGPSKGVELRNDSEGFIHEFGHAVDDYAGYLLDKNQSDLVTNSKKFIDIFKEEGSNLTSYGRTNEAEFFAEAFRLMHSTDHAERLKVQKNAPKTFQFINDQIKFIINS--   -
               SCOP domains d1yqya2 A:265-550 Anthrax toxin lethal factor, middle domain                                                                                                                                                                                                                                  d1yqya1 A:551-778 Anthrax toxin lethal factor, N- and C-terminal domains                                                                                                                                                             SCOP domains
               CATH domains 1yqyA01 A:265-301,A:385-551          1yqyA02 A:302-384 Anthrax toxin lethal factor, domain 3, chain A                   1yqyA01 A:265-301,A:385-551 Toxin ADP-ribosyltransferase; Chain A, domain 1                                                                                            1yqyA03 A:552-778 Collagenase (Catalytic Domain)                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhh...........hhhhhhhhhhhhhhh...hhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.......hhhhh.eeeeehhhhhhhhhhh...........hhhhhhhhhhh..eeee....eee...........eeeeee......eeee...eeee...eeeeeeeeeeeee..eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhh...hhhhh....eeeehhhheeeee.........hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -S-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yqy A 265 LSRYEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPIEPKKDDIIHSLSQEEKELLKRIQIDSSDFLSTEEKEFLKKLQIDIRDSLSEEEKELLNRIQVDSSNPLSEKEKEFLKKLKLDIQPYDINQRLQDTGGLIDSPSINLDVRKQYKRDIQNIDALLHQSIGSTLYNKIYLYENMNINNLTATLGADLVDSTDNTKINRGIFNEFKKNFKYSISSNYMIVDINERPALDNERLKWRIQLSPDTRAGYLENGKLILQRNIGLEIKDVQIIKQSEKEYIRIDAKVVPKSKIDTKIQEAQLNINQEWNKALGLPKYTKLITFNVHNRYASNIVESAYLILNEWKNNIQSDLIKKVTNYLVDGNGRFVFTDITLPNIAEQYTHQDEIYEQVHSKGLYVPESRSILLHGPSKGVELRNDSEGFIHEFGHAVDDYAGYLLDKNQSDLVTNSKKFIDIFKEEGSNLTSYGRTNEAEFFAEAFRLMHSTDHAERLKVQKNAPKTFQFINDQIKFIINSLV 778
                                   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       674       684       694       704       714       724       734       744       754       764       774    

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YQY)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LEF_BACAN | P15917)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0043409    negative regulation of MAPK cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the MAPKKK cascade.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0044533    positive regulation of apoptotic process in other organism    Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death by apoptosis in a second organism.
    GO:0097300    programmed necrotic cell death    A necrotic cell death process that results from the activation of endogenous cellular processes, such as signaling involving death domain receptors or Toll-like receptors.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0035897    proteolysis in other organism    The chemical reactions and pathways performed by an organism resulting in the hydrolysis of proteins in another organism by cleavage of their peptide bonds.
    GO:1903140    regulation of establishment of endothelial barrier    Any process that modulates the frequency, rate or extent of establishment of endothelial barrier.
    GO:0061136    regulation of proteasomal protein catabolic process    Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LEF_BACAN | P159171j7n 1jky 1pwp 1pwq 1pwu 1pwv 1pww 1zxv 2l0r 3kwv 4dv8 4pkq 4pkr 4pks 4pkt 4pku 4pkv 4pkw 4wf6 4xm6 4xm7 4xm8 5d1s 5d1t 5d1u

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1YQY)