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(-) Description

Title :  CRYSTAL STRUCTURE OF BLEOMYCIN-BINDING PROTEIN FROM BLEOMYCIN-PRODUCING STREPTOMYCES VERTICILLUS COMPLEXED WITH COPPER(II)-BLEOMYCIN
 
Authors :  M. Sugiyama, T. Kumagai, M. Hayashida, M. Maruyama, Y. Matoba
Date :  02 Jul 01  (Deposition) - 06 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Ligand Complex, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sugiyama, T. Kumagai, M. Hayashida, M. Maruyama, Y. Matoba
The 1. 6-A Crystal Structure Of The Copper(Ii)-Bound Bleomycin Complexed With The Bleomycin-Binding Protein From Bleomycin-Producing Streptomyces Verticillus.
J. Biol. Chem. V. 277 2311 2002
PubMed-ID: 11706014  |  Reference-DOI: 10.1074/JBC.M103278200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BLEOMYCIN-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKKTRP
    Expression System Strain: HB101
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BLMA
    Organism Scientific: STREPTOMYCES VERTICILLUS
    Organism Taxid: 29309

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1BLM2Ligand/IonBLEOMYCIN A2
2CL2Ligand/IonCHLORIDE ION
3CU2Ligand/IonCOPPER (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREBLM B:401 , CL B:501BINDING SITE FOR RESIDUE CU B 403
2AC2SOFTWARECL A:502 , BLM B:402BINDING SITE FOR RESIDUE CU A 404
3AC3SOFTWAREBLM B:401 , CU B:403 , HOH B:609BINDING SITE FOR RESIDUE CL B 501
4AC4SOFTWARECU A:404 , HOH A:613 , BLM B:402BINDING SITE FOR RESIDUE CL A 502
5AC5SOFTWAREPHE A:33 , PHE A:38 , SER A:51 , ARG A:52 , GLU A:99 , ARG A:104 , HOH A:628 , HOH A:639 , ASP B:260 , THR B:262 , TRP B:265 , TYR B:286 , ALA B:307 , ARG B:309 , GLY B:313 , CYS B:315 , CU B:403 , CL B:501 , HOH B:618 , HOH B:625 , HOH B:627 , HOH B:631 , HOH B:634 , HOH B:636 , HOH B:670 , HOH B:673 , HOH B:679 , HOH B:691 , HOH B:704BINDING SITE FOR RESIDUE BLM B 401
6AC6SOFTWAREASP A:60 , ASN A:61 , THR A:62 , TRP A:65 , TYR A:86 , PRO A:101 , ALA A:107 , ARG A:109 , GLY A:113 , CYS A:115 , CU A:404 , CL A:502 , HOH A:616 , HOH A:645 , HOH A:682 , PHE B:233 , PHE B:238 , ARG B:247 , SER B:251 , ARG B:252 , GLU B:299 , ARG B:304 , HOH B:638 , HOH B:640 , HOH B:660 , HOH B:677 , HOH B:688 , HOH B:694 , HOH B:710 , HOH B:716 , HOH B:717BINDING SITE FOR RESIDUE BLM B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JIF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JIF)

(-) Exons   (0, 0)

(no "Exon" information available for 1JIF)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:122
 aligned with Q53793_9ACTN | Q53793 from UniProtKB/TrEMBL  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
         Q53793_9ACTN     1 MVKFLGAVPVLTAVDVPANVSFWVDTLGFEKDFGDRDFAGVRRGDIRLHISRTEHQIVADNTSAWIEVTDPDALHEEWARAVSTDYADTSGPAMTPVGESPAGREFAVRDPAGNCVHFTAGE 122
               SCOP domains d1jifa_ A: Bleomycin resistance protein, BRP                                                                               SCOP domains
               CATH domains 1jifA00 A:1-122 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee.hhhhhhhhhhhh...eeeee...eeeeee..eeeeeee..hhhhhh..eeeeee.hhhhhhhhhhh............ee...eee..eeeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jif A   1 MVKFLGAVPVLTAVDVPANVSFWVDTLGFEKDFGDRDFAGVRRGDIRLHISRTEHQIVADNTSAWIEVTDPDALHEEWARAVSTDYADTSGPAMTPVGESPAGREFAVRDPAGNCVHFTAGE 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  


Chain B from PDB  Type:PROTEIN  Length:122
 aligned with Q53793_9ACTN | Q53793 from UniProtKB/TrEMBL  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
         Q53793_9ACTN     1 MVKFLGAVPVLTAVDVPANVSFWVDTLGFEKDFGDRDFAGVRRGDIRLHISRTEHQIVADNTSAWIEVTDPDALHEEWARAVSTDYADTSGPAMTPVGESPAGREFAVRDPAGNCVHFTAGE 122
               SCOP domains d1jifb_ B: Bleomycin resistance protein, BRP                                                                               SCOP domains
               CATH domains 1jifB00 B:201-322 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee.hhhhhhhhhhhh...eeeee...eeeeee..eeeeeee..hhhhhh..eeeeee.hhhhhhhhhh.............ee..........eeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jif B 201 MVKFLGAVPVLTAVDVPANVSFWVDTLGFEKDFGDRDFAGVRRGDIRLHISRTEHQIVADNTSAWIEVTDPDALHEEWARAVSTDYADTSGPAMTPVGESPAGREFAVRDPAGNCVHFTAGE 322
                                   210       220       230       240       250       260       270       280       290       300       310       320
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  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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q53793_9ACTN | Q53793)
molecular function
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
biological process
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

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 Related Entries

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

UniProtKB/TrEMBL
        Q53793_9ACTN | Q53793: 1jie 1qto

(-) Related Entries Specified in the PDB File

1ecs 1ECS CONTAINS THE SIMILAR PROTEIN(BLEOMYCIN RESISTANCE PROTEIN) UNCOMPLEXED WITH BLEOMYCIN
1ewj 1EWJ CONTAINS THE SIMILAR PROTEIN(BLEOMYCIN RESISTANCE DETERMINANT) COMPLEXED WITH METAL-FREE BLEOMYCIN
1jie 1JIE CONTAINS THE SAME PROTEIN COMPLEXED WITH METAL-FREE BLEOMYCIN
1qto 1QTO CONTAINS THE SAME PROTEIN UNCOMPLEXED WITH BLEOMYCIN