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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NEOCARZINOSTATIN 4TES1 MUTANT BOUND TESTOSTERONE HEMISUCCINATE.
 
Authors :  A. Drevelle, M. Graille, B. Heyd, I. Sorel, N. Ulryck, F. Pecorari, M. Desmadril, H. Van Tilbeurgh, P. Minard
Date :  06 Jan 06  (Deposition) - 22 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antibiotic, Phage-Display, Hapten Binding, Neocarzinostatin, Antimicrobial, Dna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Drevelle, M. Graille, B. Heyd, I. Sorel, N. Ulryck, F. Pecorari, M. Desmadril, H. Van Tilbeurgh, P. Minard
Structures Of In Vitro Evolved Binding Sites On Neocarzinostatin Scaffold Reveal Unanticipated Evolutionary Pathways.
J. Mol. Biol. V. 358 455 2006
PubMed-ID: 16529771  |  Reference-DOI: 10.1016/J.JMB.2006.02.002
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEOCARZINOSTATIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BLR(DE3)PLYSS
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: STREPTOMYCES CARZINOSTATICUS
    Organism Taxid: 1897
    Synonym: NCS, MITOMALCIN, MMC

 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
1TH22Ligand/IonTESTOSTERONE HEMISUCCINATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:1033 , SER A:1047 , PRO A:1049 , TRP A:1078 , ARG A:1098 , ASP A:1099 , ALA A:1100 , LEU A:1101 , SER A:1102 , SER B:2011 , TRP B:2033 , TH2 B:2120BINDING SITE FOR RESIDUE TH2 A1120
2AC2SOFTWARETRP A:1033 , TH2 A:1120 , TRP B:2033 , SER B:2047 , PRO B:2049 , TRP B:2078 , ALA B:2100 , SER B:2102BINDING SITE FOR RESIDUE TH2 B2120

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CBT)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:1008 -Pro A:1009
2Thr B:2008 -Pro B:2009

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CBT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CBT)

(-) Exons   (0, 0)

(no "Exon" information available for 2CBT)

(-) 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:111
 aligned with NCZS_STRCZ | P0A3R9 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:111
                                    45        55        65        75        85        95       105       115       125       135       145 
          NCZS_STRCZ     36 APTATVTPSSGLSDGTVVKVAGAGLQAGTAYDVGQCAWVDTGVLACNPADFSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISF  146
               SCOP domains d2cbta_ A: automated matches                                                                                    SCOP domains
               CATH domains 2cbtA00 A:1002-1112  [code=2.60.40.230, no name defined]                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...........eeeeeee......eeeeeeeeeee..eeee.hhhheeee......eeeeee....eeeee....eeeee.......eeeee.........ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                2cbt A 1002 APTATVTPSSGLSDGTVVKVAGAGLQAGTAYWVAQSAWVDTGVYASNPADISSVTADANGSASTSLTVRRSFEGFLWDGTRWGTVDCTTAACHVTLRDALSNGPEGVAISF 1112
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111 


Chain B from PDB  Type:PROTEIN  Length:111
 aligned with NCZS_STRCZ | P0A3R9 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:111
                                    45        55        65        75        85        95       105       115       125       135       145 
          NCZS_STRCZ     36 APTATVTPSSGLSDGTVVKVAGAGLQAGTAYDVGQCAWVDTGVLACNPADFSSVTADANGSASTSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGPEGVAISF  146
               SCOP domains d2cbtb_ B: automated matches                                                                                    SCOP domains
               CATH domains 2cbtB00 B:2002-2112  [code=2.60.40.230, no name defined]                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..........eeeeeeee......eeeeeeee.......ee.....eeee.......eeeeee...eeeee......eee......eeeeee.........ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                2cbt B 2002 APTATVTPSSGLSDGTVVKVAGAGLQAGTAYWVAQSAWVDTGVYASNPADISSVTADANGSASTSLTVRRSFEGFLWDGTRWGTVDCTTAACHVTLRDALSNGPEGVAISF 2112
                                  2011      2021      2031      2041      2051      2061      2071      2081      2091      2101      2111
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CBT)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NCZS_STRCZ | P0A3R9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NCZS_STRCZ | P0A3R9: 1j5h 1j5i 1nco 1noa 1o5p 2cbm 2cbo 2cbq 2g0k 2g0l

(-) Related Entries Specified in the PDB File

1j5h SOLUTION STRUCTURE OF APO-NEOCARZINOSTATIN
1j5i SOLUTION STRUCTURE OF A NOVEL CHROMOPROTEIN DERIVED FROMAPO-NEOCARZINOSTATIN AND A SYNTHETIC CHROMOPHORE
1kvh NCSI-GB-BULGE-DNA COMPLEX INDUCED FORMATION OF A DNA BULGESTRUCTURE BY A MOLECULAR WEDGE LIGAND-POST-ACTIVATEDNEOCARZINOSTATIN CHROMOPHORE
1mp7 A THIRD COMPLEX OF POST-ACTIVATED NEOCARZINOSTATINCHROMOPHORE WITH DNA. BULGE DNA BINDING FROM THE MINORGROOVE
1nco HOLO-NEOCARZINOSTATIN (CONTAINING CHROMOPHORE) COMPLEX WITH APO-CARZINOSTATIN (CONTAINING MPD)
1noa NEOCARZINOSTATIN
1o5p SOLUTION STRUCTURE OF HOLO-NEOCARZINOSTATIN
2cbm CRYSTAL STRUCTURE OF THE APO-FORM OF A NEOCARZINOSTATIN MUTANT EVOLVED TO BIND TESTOSTERONE.
2cbo CRYSTAL STRUCTURE OF THE NEOCARZINOSTATIN 3TES24 MUTANT BOUND TO TESTOSTERONE HEMISUCCINATE.
2cbq CRYSTAL STRUCTURE OF THE NEOCARZINOSTATIN 1TES15 MUTANT BOUND TO TESTOSTERONE HEMISUCCINATE.