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(-) Description

Title :  CRYSTAL STRUCTURE OF CLAVULANIC ACID BOUND TO E166A VARIANT OF SHV-1 BETA-LACTAMASE
 
Authors :  P. S. Padayatti, M. S. Helfand, M. A. Totir, M. P. Carey, P. R. Carey, R. A. Bonomo, F. Van Den Akker
Date :  28 Jun 05  (Deposition) - 02 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.43
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Lactamase, Beta-Lactam Hydrolase, Penicillinase, Detergent Binding, Inhibitor Design, Covalent Intermediate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. S. Padayatti, M. S. Helfand, M. A. Totir, M. P. Carey, P. R. Carey, R. A. Bonomo, F. Van Den Akker
High Resolution Crystal Structures Of The Trans-Enamine Intermediates Formed By Sulbactam And Clavulanic Acid And E166A Shv-1 {Beta}-Lactamase.
J. Biol. Chem. V. 280 34900 2005
PubMed-ID: 16055923  |  Reference-DOI: 10.1074/JBC.M505333200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE SHV-1
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BLA, SHV1
    Mutation: YES
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573
    Synonym: PIT-2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2MA42Ligand/IonCYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE
3TEM1Ligand/IonN-(2-HYDROXY-4-OXO-BUTYL)-N-(3-OXO-TRANSPROPENYL)AMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:69 , SER A:70 , ASN A:170 , GLY A:236 , ALA A:237 , EPE A:600 , HOH A:896 , HOH A:906BINDING SITE FOR RESIDUE TEM A 501
2AC2SOFTWAREARG A:93 , HIS A:96 , ARG A:98 , ILE A:221 , VAL A:224 , PRO A:226 , ALA A:248 , VAL A:261 , ILE A:263 , ALA A:280 , ALA A:284 , GLU A:288 , HOH A:614 , HOH A:633 , HOH A:726 , HOH A:752 , HOH A:860BINDING SITE FOR RESIDUE MA4 A 400
3AC3SOFTWAREARG A:244 , ILE A:279BINDING SITE FOR RESIDUE MA4 A 401
4AC4SOFTWARESER A:70 , SER A:130 , VAL A:216 , LYS A:234 , THR A:235 , GLY A:236 , ARG A:244 , TEM A:501BINDING SITE FOR RESIDUE EPE A 600

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:77 -A:123

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A49)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A49)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_APS00146 Beta-lactamase class-A active site.BLA1_ECOLX62-77  1A:66-81
BLA1_KLEPN62-77  1A:66-81

(-) Exons   (0, 0)

(no "Exon" information available for 2A49)

(-) 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:265
 aligned with BLA1_ECOLX | P0AD63 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:265
                                    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     
           BLA1_ECOLX    22 SPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR 286
               SCOP domains d2a49a_ A: beta-Lactamase, class A                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2a49A00 A:26-292 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee..hhhhh.....hhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------BETA_LACTAMASE_A----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a49 A  26 SPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWATELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR 292
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287     
                                                                                                                                                                                                                                              238|         252|                                      
                                                                                                                                                                                                                                               240          254                                      


Chain A from PDB  Type:PROTEIN  Length:265
 aligned with BLA1_KLEPN | P0AD64 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:265
                                    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     
           BLA1_KLEPN    22 SPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR 286
               SCOP domains d2a49a_ A: beta-Lactamase, class A                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2a49A00 A:26-292 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.eeeeeeee.....eeeee.....ee...hhhhhhhhhhhhhhhh.......ee..hhhhh.....hhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------BETA_LACTAMASE_A----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a49 A  26 SPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVVLCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAAAITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWATELNEALPGDARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVLPAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQQIAGIGAALIEHWQR 292
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287     
                                                                                                                                                                                                                                              238|         252|                                      
                                                                                                                                                                                                                                               240          254
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A49)

(-) Gene Ontology  (4, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BLA1_KLEPN | P0AD64)
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 A   (BLA1_ECOLX | P0AD63)
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.

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  2a49
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  BLA1_KLEPN | P0AD64
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 Related Entries

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

UniProtKB/Swiss-Prot
        BLA1_ECOLX | P0AD63: 1ong 1q2p 1rcj 1shv 1tdg 1tdl 2a3u
        BLA1_KLEPN | P0AD64: 1ong 1q2p 1rcj 1shv 1tdg 1tdl 1vm1 2a3u 2g2u 2g2w 2h0t 2h0y 2h10 2h5s 2zd8 3c4o 3c4p 3d4f 3mke 3mkf 3mxr 3mxs 3n4i 3oph 3opl 3opp 3opr 3v50 3v5m 4fcf 4fd8 4fh2 4fh4 4gd6 4gd8 4gdb 4jpm 4mbf 4mbh 4mbk 4r3b 4zam 5ee8

(-) Related Entries Specified in the PDB File

1rcj TAZOBACTAM BOUND E166A SHV-1 STRUCTURE
2a3u SULBACTAM BOUND E166A SHV-1 STRUCTURE