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(-) Description

Title :  CRYSTAL STRUCTURE OF CLASS C BETA-LACTAMASE ACT-1
 
Authors :  A. Shimizu-Ibuka, H. Sakai, M. Galleni
Date :  02 Nov 07  (Deposition) - 23 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Two-Domain Structure, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Shimizu-Ibuka, C. Bauvois, H. Sakai, M. Galleni
Structure Of The Plasmid-Mediated Class C Beta-Lactamase Act-1
Acta Crystallogr. , Sect. F V. 64 334 2008
PubMed-ID: 18453698  |  Reference-DOI: 10.1107/S1744309108008531
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE ACT-1
    Chains: A, B, C, D
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES IN DATABASE 23-381
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2ZC7)

(-) Sites  (0, 0)

(no "Site" information available for 2ZC7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZC7)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp A:276 -Pro A:277
2Trp B:276 -Pro B:277
3Trp C:276 -Pro C:277
4Trp D:276 -Pro D:277

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZC7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZC7)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZC7)

(-) 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:359
 aligned with Q48428_KLEPN | Q48428 from UniProtKB/TrEMBL  Length:381

    Alignment length:359
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372         
         Q48428_KLEPN    23 PMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVKDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL 381
               SCOP domains d2zc7a_ A: automated matches                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2zc7A00 A:2-360 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhh.....hhhhh..hhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhhh.hhhhhhhhhh.............hhhhhhhh..ee....ee......hhhhhh..eehhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.eeeee..eee....eeee...hhhhhhhhhhhhhhh..ee.eeeeeee.....eeeeeeee....eeeeeee....eeeeeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zc7 A   2 PMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVKDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL 360
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351         


Chain B from PDB  Type:PROTEIN  Length:359
 aligned with Q48428_KLEPN | Q48428 from UniProtKB/TrEMBL  Length:381

    Alignment length:359
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372         
         Q48428_KLEPN    23 PMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVKDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL 381
               SCOP domains d2zc7b_ B: automated matches                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2zc7B00 B:2-360 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhhh....hhhhh..hhhhhhh...............hhhhhhhhhhh.........ee..hhhhhhhhhhhhh.....hhhhhhhhhh.............hhhhh.....ee....ee......hhhhhhh.eehhhhhhhhhhhhhh.....hhhhhhhhhhhh.eeeee..eee....eeee...hhhhhhhhhhhhhhh..ee.eeeeeee.....eeeeeeee....eeeeeee....eeeeeee....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zc7 B   2 PMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVKDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL 360
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351         


Chain C from PDB  Type:PROTEIN  Length:359
 aligned with Q48428_KLEPN | Q48428 from UniProtKB/TrEMBL  Length:381

    Alignment length:359
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372         
         Q48428_KLEPN    23 PMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVKDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL 381
               SCOP domains d2zc7c_ C: automated matches                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2zc7C00 C:2-360 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhh.....hhhhh..hhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhhh.hhhhhhhhhh.............hhhhhhhh..ee....ee......hhhhhh..eehhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.eeeee..eee....eeee...hhhhhhhhhhhhhhh..ee.eeeeeee.....eeeeeeee....eeeeeeehhhheeeeeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zc7 C   2 PMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVKDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL 360
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351         


Chain D from PDB  Type:PROTEIN  Length:359
 aligned with Q48428_KLEPN | Q48428 from UniProtKB/TrEMBL  Length:381

    Alignment length:359
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372         
         Q48428_KLEPN    23 PMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVKDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL 381
               SCOP domains d2zc7d_ D: automated matches                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2zc7D00 D:2-360 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                                 CATH domains
           Pfam domains (1) ----------Beta-lactamase-2zc7D01 D:12-360                                                                                                                                                                                                                                                                                                                               Pfam domains (1)
           Pfam domains (2) ----------Beta-lactamase-2zc7D02 D:12-360                                                                                                                                                                                                                                                                                                                               Pfam domains (2)
           Pfam domains (3) ----------Beta-lactamase-2zc7D03 D:12-360                                                                                                                                                                                                                                                                                                                               Pfam domains (3)
           Pfam domains (4) ----------Beta-lactamase-2zc7D04 D:12-360                                                                                                                                                                                                                                                                                                                               Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh...eeeeee....eeeee..eee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhh............hhhhhhh...............hhhhhhhhhhh.........ee..hhhhhhhhhhhhh.....hhhhhhhhhh.............hhhhhhhh..ee....ee......hhhhhh..eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.eeeee..eee....eeee...hhhhhhhhhhhhhhh..ee.eeeeeee.....eeeeeeee....eeeeeeehhhheeeeeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zc7 D   2 PMSEKQLAEVVERTVTPLMKAQAIPGMAVAVIYEGQPHYFTFGKADVAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLGDPVTKYWPELTGKQWQGIRMLDLATYTAGGLPLQVPDEVKDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMSYEQAITTRVFKPLKLDHTWINVPKAEEAHYAWGYRDGKAVHVSPGMLDAEAYGVKTNVQDMASWVMVNMKPDSLQDNSLRKGLTLAQSRYWRVGAMYQGLGWEMLNWPVDAKTVVEGSDNKVALAPLPAREVNPPAPPVNASWVHKTGSTGGFGSYVAFIPEKQLGIVMLANKSYPNPARVEAAYRILSAL 360
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351
   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, 4)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Beta-lactamase (210)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q48428_KLEPN | Q48428)
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: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:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

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 Related Entries

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