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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-LACTAMSE INHIBITORY PROTEIN-I (BLIP-I) IN COMPLEX WITH TEM-1 BETA-LACTAMASE
 
Authors :  D. C. Lim, M. Gretes, N. C. J. Strynadka
Date :  15 Mar 09  (Deposition) - 31 Mar 09  (Release) - 02 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Protein-Protein Complex, Antibiotic Resistance, Hydrolase, Plasmid, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Gretes, D. C. Lim, L. De Castro, S. E. Jensen, S. G. Kang, K. J. Lee, N. C. Strynadka
Insights Into Positive And Negative Requirements For Protein-Protein Interactions By Crystallographic Analysis Of The Beta-Lactamase Inhibitory Proteins Blip, Blip-I, And Blp.
J. Mol. Biol. V. 389 289 2009
PubMed-ID: 19332077  |  Reference-DOI: 10.1016/J.JMB.2009.03.058
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - B-LACTAMASE
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC118
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AMP, BLA
    Organism Scientific: ESCHERICHIA SP. SFLU5
    Organism Taxid: 299586
    Strain: CB86134
 
Molecule 2 - BETA-LACTAMASE INHIBITORY PROTEIN BLIP-I
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A(+)
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BLIA
    Organism Common: STREPTOMYCES HYDROGENANS
    Organism Scientific: STREPTOMYCES EXFOLIATUS
    Organism Taxid: 1905
    Strain: SMF19

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN B:109 , TYR B:126 , SER B:140 , PHE B:141 , HIS B:142 , HOH B:379BINDING SITE FOR RESIDUE PO4 B 1
2AC2SOFTWARETHR B:59 , ASP B:60 , GLU B:61 , HOH B:304BINDING SITE FOR RESIDUE PO4 B 158
3AC3SOFTWAREGLY C:92 , ARG C:120 , HOH C:294BINDING SITE FOR RESIDUE PO4 C 2
4AC4SOFTWAREGLN D:109 , TYR D:126 , SER D:140 , HIS D:142 , HOH D:387BINDING SITE FOR RESIDUE PO4 D 158

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:77 -A:123
2B:31 -B:43
3B:106 -B:128
4C:77 -C:123
5D:31 -D:43
6D:106 -D:128

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:166 -Pro A:167
2Trp B:116 -Pro B:117
3Glu C:166 -Pro C:167
4Trp D:116 -Pro D:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GMW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GMW)

(-) Exons   (0, 0)

(no "Exon" information available for 3GMW)

(-) 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:261
 aligned with A5PHA6_9ESCH | A5PHA6 from UniProtKB/TrEMBL  Length:286

    Alignment length:261
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285 
         A5PHA6_9ESCH    26 ETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW 286
               SCOP domains d3gmwa_ A: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3gmwA00 A:28-288 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee..hhhhh.....hhhhhh...eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gmw A  28 ETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW 288
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287 


Chain B from PDB  Type:PROTEIN  Length:154
 aligned with Q9KJ90_STREX | Q9KJ90 from UniProtKB/TrEMBL  Length:186

    Alignment length:154
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    
         Q9KJ90_STREX    33 FSAEKYEQIQFGMTFDEVWEIGGGEAACDTGGVIGDSILCFTESGDYAPYGGFSFTDEGELWSKRNEYLYKAKTPSVKLSHYNRTALGMTEAQLWAAVPKDSCVSQGESYPNWPAKTGFEEKYYCAAATGLFPPSASFHLTDGVLTYRYQRSLT 186
               SCOP domains d3gmwb_ B: automated matches                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh....hhhhhhhhhhhhhheee.hhhh..eeee........eeeeee.....eeeeeee..........hhhhhhh.....hhhhhhhhhhhh.eeeeeee..........eeeeeee........eeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gmw B   4 FSAEKYEQIQFGMTFDEVWEIGGGEAACDTGGVIGDSILCFTESGDYAPYGGFSFTDEGELWSKRNEYLYKAKTPSVKLSHYNRTALGMTEAQLWAAVPKDSCVSQGESYPNWPAKTGFEEKYYCAAATGLFPPSASFHLTDGVLTYRYQRSLT 157
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153    


Chain C from PDB  Type:PROTEIN  Length:261
 aligned with A5PHA6_9ESCH | A5PHA6 from UniProtKB/TrEMBL  Length:286

    Alignment length:261
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285 
         A5PHA6_9ESCH    26 ETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW 286
               SCOP domains d3gmwc_ C: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3gmwC00 C:28-288 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee..hhhhh.....hhhhhh...eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh............hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gmw C  28 ETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW 288
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287 


Chain D from PDB  Type:PROTEIN  Length:156
 aligned with Q9KJ90_STREX | Q9KJ90 from UniProtKB/TrEMBL  Length:186

    Alignment length:156
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      
         Q9KJ90_STREX    31 SGFSAEKYEQIQFGMTFDEVWEIGGGEAACDTGGVIGDSILCFTESGDYAPYGGFSFTDEGELWSKRNEYLYKAKTPSVKLSHYNRTALGMTEAQLWAAVPKDSCVSQGESYPNWPAKTGFEEKYYCAAATGLFPPSASFHLTDGVLTYRYQRSLT 186
               SCOP domains d3gmwd_ D: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhh....hhhhhhhhhhhhhhee.hhhhh..eeee........eeeeee.....eeeeeee..........hhhhhhh.....hhhhhhhhhhhh.eeeeeee..........eeeeeee........eeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gmw D   2 SGFSAEKYEQIQFGMTFDEVWEIGGGEAACDTGGVIGDSILCFTESGDYAPYGGFSFTDEGELWSKRNEYLYKAKTPSVKLSHYNRTALGMTEAQLWAAVPKDSCVSQGESYPNWPAKTGFEEKYYCAAATGLFPPSASFHLTDGVLTYRYQRSLT 157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GMW)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (A5PHA6_9ESCH | A5PHA6)
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.
biological process
    GO:0030655    beta-lactam antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins.
    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.

Chain B,D   (Q9KJ90_STREX | Q9KJ90)

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  3gmw
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 Related Entries

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

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        Q9KJ90_STREX | Q9KJ90: 3gmv

(-) Related Entries Specified in the PDB File

3gmu 3gmv 3gmx 3gmy