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(-) Description

Title :  THE STRUCTURE OF IMP-1 COMPLEXED WITH THE DETECTING REAGENT (DANSYLC4SH) BY A FLUORESCENT PROBE
 
Authors :  H. Kurosaki, Y. Yamaguchi, H. Yasuzawa, W. Jin, Y. Yamagata, Y. Arakawa
Date :  01 May 06  (Deposition) - 28 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.43
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Metallo-Beta-Lactamase, Protein-Inhibitor Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Kurosaki, Y. Yamaguchi, H. Yasuzawa, W. Jin, Y. Yamagata, Y. Arakawa
Probing, Inhibition, And Crystallographic Characterization Of Metallo-Beta-Lactamase (Imp-1) With Fluorescent Agents Containing Dansyl And Thiol Groups
Chemmedchem V. 1 969 2006
PubMed-ID: 16937423  |  Reference-DOI: 10.1002/CMDC.200600115
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE IMP-1
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET9A-D-IMP
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET9A
    Expression System Vector Type: PLASMID
    Gene: BLAIMP-1
    Organism Scientific: SERRATIA MARCESCENS
    Organism Taxid: 615
    Synonym: BETA-LACTAMASE, TYPE II, PENICILLINASE, BLAIMP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1C4H2Ligand/IonN-[4-({[5-(DIMETHYLAMINO)-1-NAPHTHYL]SULFONYL}AMINO)BUTYL]-3-SULFANYLPROPANAMIDE
2ZN4Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:77 , HIS A:79 , HIS A:139 , C4H A:601BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREASP A:81 , CYS A:158 , HIS A:197 , C4H A:601BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWAREHIS B:77 , HIS B:79 , HIS B:139 , C4H B:602BINDING SITE FOR RESIDUE ZN B 503
4AC4SOFTWAREASP B:81 , CYS B:158 , HIS B:197 , C4H B:602BINDING SITE FOR RESIDUE ZN B 504
5AC5SOFTWAREVAL A:25 , TRP A:28 , VAL A:31 , HIS A:77 , HIS A:79 , ASP A:81 , HIS A:139 , CYS A:158 , LYS A:161 , TYR A:163 , GLY A:164 , LEU A:165 , GLY A:166 , HIS A:197 , ZN A:501 , ZN A:502 , HOH A:607 , HOH A:663 , HOH A:674 , GLU B:211 , GLN B:212BINDING SITE FOR RESIDUE C4H A 601
6AC6SOFTWAREGLU A:211 , GLN A:212 , TRP B:28 , VAL B:31 , HIS B:79 , ASP B:81 , HIS B:139 , CYS B:158 , LYS B:161 , TYR B:163 , GLY B:164 , GLY B:166 , HIS B:197 , ZN B:503 , ZN B:504 , HOH B:637 , HOH B:648 , HOH B:658 , HOH B:663BINDING SITE FOR RESIDUE C4H B 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DOO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLAB_SERMA92-111
 		  2A:74-93
B:74-93
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLAB_SERMA167-179
 		  2A:149-161
B:149-161

(-) Exons   (0, 0)

(no "Exon" information available for 2DOO)

(-) 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:216
 aligned with BLAB_SERMA | P52699 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:216
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      
           BLAB_SERMA    22 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNE 237
               SCOP domains d2dooa_ A: Zn metallo-beta-lactamase                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeeee.....eeeeeeeeee...eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeee.................hhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------BETA_LACTAMASE_B_1  -------------------------------------------------------BETA_LACTAMAS---------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2doo A   4 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNE 219
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213      


Chain A from PDB  Type:PROTEIN  Length:216
 aligned with Q6BCU6_SERMA | Q6BCU6 from UniProtKB/TrEMBL  Length:238

    Alignment length:216
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223      
         Q6BCU6_SERMA    14 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNE 229
               SCOP domains d2dooa_ A: Zn metallo-beta-lactamase                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeeee.....eeeeeeeeee...eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeee.................hhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2doo A   4 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNE 219
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213      


Chain B from PDB  Type:PROTEIN  Length:216
 aligned with BLAB_SERMA | P52699 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:216
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      
           BLAB_SERMA    22 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNE 237
               SCOP domains d2doob_ B: Zn metallo-beta-lactamase                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeeeee...eeeeeeeeeee...eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeee.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------BETA_LACTAMASE_B_1  -------------------------------------------------------BETA_LACTAMAS---------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2doo B   4 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNE 219
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213      


Chain B from PDB  Type:PROTEIN  Length:216
 aligned with Q6BCU6_SERMA | Q6BCU6 from UniProtKB/TrEMBL  Length:238

    Alignment length:216
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223      
         Q6BCU6_SERMA    14 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNE 229
               SCOP domains d2doob_ B: Zn metallo-beta-lactamase                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeeeee...eeeeeeeeeee...eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeee.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2doo B   4 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNE 219
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DOO)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BLAB_SERMA | P52699)
molecular function
    GO:0008800    beta-lactamase activity    Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0017001    antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain A,B   (Q6BCU6_SERMA | Q6BCU6)
molecular function
    GO:0008800    beta-lactamase activity    Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0017001    antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    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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  2doo
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 Related Entries

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

UniProtKB/Swiss-Prot
        BLAB_SERMA | P52699: 1dd6 1jje 1jjt 1vgn 1wuo 1wup 4c1f 4c1g 5ev6 5ev8 5ewa 5hh4

(-) Related Entries Specified in the PDB File

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