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(-) Description

Title :  CRYSTAL STRUCTURE OF BLEOMYCIN-BINDING PROTEIN COMPLEXED WITH BLEOMYCIN
 
Authors :  M. Maruyama, T. Kumagai, Y. Matoba, Y. Hata, M. Sugiyama
Date :  26 Apr 00  (Deposition) - 26 Apr 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Bleomycin-Binding Protein, Bleomycin, Antibiotics Resistance, Homodimer, Antibiotic Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Maruyama, T. Kumagai, Y. Matoba, M. Hayashida, T. Fujii, Y. Hata, M. Sugiyama
Crystal Structures Of The Transposon Tn5-Carried Bleomycin Resistance Determinant Uncomplexed And Complexed With Bleomycin.
J. Biol. Chem. V. 276 9992 2001
PubMed-ID: 11134052  |  Reference-DOI: 10.1074/JBC.M009874200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BLEOMYCIN RESISTANCE DETERMINANT
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: STREPTOMYCES VERTICILLUS
    Expression System Plasmid: PKKTRP
    Expression System Taxid: 29309
    Expression System Vector Type: PLASMID
    Fragment: CORE DOMAIN
    Gene: TRANSPOSON TN5
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573
    Other Details: CULTURE BROTH

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1BLM8Ligand/IonBLEOMYCIN A2
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1BLM2Ligand/IonBLEOMYCIN A2
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1BLM2Ligand/IonBLEOMYCIN A2
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1BLM2Ligand/IonBLEOMYCIN A2
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1BLM2Ligand/IonBLEOMYCIN A2

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:55 , LEU A:56 , ALA A:57 , SER A:58 , TRP A:59 , PHE A:60 , SER A:61 , ARG A:65 , SER A:85 , SER A:86 , GLY A:87 , ARG A:90 , TRP A:99 , GLY A:111 , LEU A:113 , ARG A:115 , ASN A:119 , GLU A:120 , PHE B:30 , TRP B:35 , HOH B:826BINDING SITE FOR RESIDUE BLM A 1001
2AC2SOFTWAREPHE A:30 , TRP A:35 , ILE A:37 , PRO B:55 , LEU B:56 , ALA B:57 , SER B:58 , TRP B:59 , PHE B:60 , SER B:61 , ARG B:65 , SER B:85 , SER B:86 , GLY B:87 , ARG B:90 , TRP B:99 , GLY B:111 , LEU B:113 , ARG B:115 , ASN B:119 , GLU B:120 , HOH B:816BINDING SITE FOR RESIDUE BLM B 1002
3AC3SOFTWAREPHE C:30 , GLY C:34 , TRP C:35 , HOH C:836 , PRO D:55 , LEU D:56 , ALA D:57 , SER D:58 , TRP D:59 , PHE D:60 , SER D:61 , ARG D:65 , SER D:85 , SER D:86 , ARG D:90 , TRP D:99 , GLY D:111 , LEU D:113 , ARG D:115 , ILE D:117 , ASN D:119 , GLU D:120BINDING SITE FOR RESIDUE BLM D 1003
4AC4SOFTWAREPRO C:55 , LEU C:56 , SER C:58 , TRP C:59 , PHE C:60 , SER C:61 , ARG C:65 , SER C:85 , SER C:86 , GLY C:87 , ARG C:90 , TRP C:99 , GLY C:111 , LEU C:113 , ARG C:115 , ASN C:119 , GLU C:120 , PHE D:30 , TRP D:35 , HOH D:846BINDING SITE FOR RESIDUE BLM C 1004
5AC5SOFTWAREPRO E:55 , LEU E:56 , ALA E:57 , SER E:58 , TRP E:59 , PHE E:60 , SER E:61 , ARG E:65 , SER E:86 , GLY E:87 , ARG E:90 , TRP E:99 , GLY E:111 , LEU E:113 , ARG E:115 , ASN E:119 , HOH E:1826 , PHE F:30 , TRP F:35 , PHE F:48BINDING SITE FOR RESIDUE BLM E 2001
6AC6SOFTWAREPHE E:30 , GLY E:34 , TRP E:35 , PHE E:48 , PRO F:55 , LEU F:56 , SER F:58 , TRP F:59 , PHE F:60 , SER F:61 , ARG F:65 , SER F:85 , ARG F:90 , TRP F:99 , GLY F:111 , LEU F:113 , ARG F:115 , ILE F:117 , ASN F:119 , GLU F:120 , HOH F:1816BINDING SITE FOR RESIDUE BLM F 2002
7AC7SOFTWAREPHE G:30 , TRP G:35 , PHE G:48 , HOH G:1836 , PRO H:55 , LEU H:56 , ALA H:57 , SER H:58 , TRP H:59 , PHE H:60 , SER H:61 , ARG H:65 , SER H:85 , SER H:86 , GLY H:87 , ARG H:90 , TRP H:99 , MET H:103 , ALA H:105 , GLY H:111 , LEU H:113 , ARG H:115BINDING SITE FOR RESIDUE BLM H 2003
8AC8SOFTWAREPRO G:55 , LEU G:56 , ALA G:57 , SER G:58 , TRP G:59 , PHE G:60 , SER G:61 , ARG G:65 , SER G:85 , SER G:86 , GLY G:87 , ARG G:90 , TRP G:99 , MET G:103 , ALA G:105 , GLY G:111 , LEU G:113 , ARG G:115 , ASN G:119 , HOH G:1846 , PHE H:30 , TRP H:35 , ILE H:37BINDING SITE FOR RESIDUE BLM G 2004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Tyr A:88 -Pro A:89
2Tyr B:88 -Pro B:89
3Tyr C:88 -Pro C:89
4Tyr D:88 -Pro D:89
5Tyr E:88 -Pro E:89
6Tyr F:88 -Pro F:89
7Tyr G:88 -Pro G:89
8Tyr H:88 -Pro H:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1EWJ)

(-) 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:119
 aligned with BLE_KLEPN | P13081 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
            BLE_KLEPN     2 TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNE 120
               SCOP domains d1ewja_ A: Bleomycin resistance protein, BRP                                                                            SCOP domains
               CATH domains 1ewjA00 A:2-120 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhhhhhhh...eeeee...eeeeee..eeeeeee...........eeeeee.hhhhhhhhhhhh..........eeeeeee.....eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1ewj A   2 TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNE 120
                                    11        21        31        41        51        61        71        81        91       101       111         


Chain B from PDB  Type:PROTEIN  Length:119
 aligned with BLE_KLEPN | P13081 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
            BLE_KLEPN     2 TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNE 120
               SCOP domains d1ewjb_ B: Bleomycin resistance protein, BRP                                                                            SCOP domains
               CATH domains 1ewjB00 B:2-120 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhhhhhhh...eeeee...eeeeee..eeeeeee...........eeeeee.hhhhhhhhhhhh..........eeeeeee.....eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1ewj B   2 TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNE 120
                                    11        21        31        41        51        61        71        81        91       101       111         


Chain C from PDB  Type:PROTEIN  Length:119
 aligned with BLE_KLEPN | P13081 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
            BLE_KLEPN     2 TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNE 120
               SCOP domains d1ewjc_ C: Bleomycin resistance protein, BRP                                                                            SCOP domains
               CATH domains 1ewjC00 C:2-120 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhhhh...eeeee...eeeeee..eeeeeee...........eeeeee.hhhhhhhhhhhh..........eeeeeee.....eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1ewj C   2 TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNE 120
                                    11        21        31        41        51        61        71        81        91       101       111         


Chain D from PDB  Type:PROTEIN  Length:119
 aligned with BLE_KLEPN | P13081 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
            BLE_KLEPN     2 TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNE 120
               SCOP domains d1ewjd_ D: Bleomycin resistance protein, BRP                                                                            SCOP domains
               CATH domains 1ewjD00 D:2-120 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.hhhhhhhhhhh...eeeee...eeeeee..eeeeeee...........eeeeee.hhhhhhhhhhhh..........eeeeeee.....eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1ewj D   2 TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNE 120
                                    11        21        31        41        51        61        71        81        91       101       111         


Chain E from PDB  Type:PROTEIN  Length:119
 aligned with BLE_KLEPN | P13081 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
            BLE_KLEPN     2 TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNE 120
               SCOP domains d1ewje_ E: Bleomycin resistance protein, BRP                                                                            SCOP domains
               CATH domains 1ewjE00 E:2-120 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee.hhhhhhhhhhh...eeeee....eeeee..eeeeeee...........eeeeee.hhhhhhhhhhhh..........eeeeeee.....eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1ewj E   2 TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNE 120
                                    11        21        31        41        51        61        71        81        91       101       111         


Chain F from PDB  Type:PROTEIN  Length:119
 aligned with BLE_KLEPN | P13081 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
            BLE_KLEPN     2 TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNE 120
               SCOP domains d1ewjf_ F: Bleomycin resistance protein, BRP                                                                            SCOP domains
               CATH domains 1ewjF00 F:2-120 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhhhhhhh...eeeee...eeeeee..eeeeeee...........eeeeee.hhhhhhhhhhhh..........eeeeeee.....eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1ewj F   2 TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNE 120
                                    11        21        31        41        51        61        71        81        91       101       111         


Chain G from PDB  Type:PROTEIN  Length:119
 aligned with BLE_KLEPN | P13081 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
            BLE_KLEPN     2 TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNE 120
               SCOP domains d1ewjg_ G: Bleomycin resistance protein, BRP                                                                            SCOP domains
               CATH domains 1ewjG00 G:2-120 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhhhhhhh...eeeee....eeeee..eeeeeee...........eeeeee.hhhhhhhhhhhh..........eeeeeee.....eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1ewj G   2 TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNE 120
                                    11        21        31        41        51        61        71        81        91       101       111         


Chain H from PDB  Type:PROTEIN  Length:119
 aligned with BLE_KLEPN | P13081 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
            BLE_KLEPN     2 TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNE 120
               SCOP domains d1ewjh_ H: Bleomycin resistance protein, BRP                                                                            SCOP domains
               CATH domains 1ewjH00 H:2-120 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.eee.hhhhhhhhhhh...eeeee...eeeeee..eeeeeee...........eeeeee.hhhhhhhhhhhh..........eeeeeee.....eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1ewj H   2 TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGGTMAALVDPDGTLLRLIQNE 120
                                    11        21        31        41        51        61        71        81        91       101       111
   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  (1, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 8)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (BLE_KLEPN | P13081)
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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  1ewj
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    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BLE_KLEPN | P13081: 1ecs 1mh6 1niq

(-) Related Entries Specified in the PDB File

1byl 1BYL CONTAINS THE FREE FORM OF THE HOMOLOGOUS PROTEIN
1ecs 1ECS CONTAINS THE FREE FORM OF THE SAME PROTEIN
1qto 1QTO CONTAINS THE FREE FORM OF THE HOMOLOGOUS PROTEIN