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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-LACTAMASE PENP MUTANT-E166H
 
Authors :  X. Pan, Y. Zhao
Date :  21 Jun 16  (Deposition) - 25 Jan 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.24
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Pan, Y. He, J. Lei, X. Huang, Y. Zhao
Crystallographic Snapshots Of Class A Beta-Lactamase Catalysis Reveal Structural Changes That Facilitate Beta-Lactam Hydrolysis
J. Biol. Chem. V. 292 4022 2017
PubMed-ID: 28100776  |  Reference-DOI: 10.1074/JBC.M116.764340

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 43-307
    Gene: PENP, BLAP
    Mutation: YES
    Organism Scientific: BACILLUS LICHENIFORMIS
    Organism Taxid: 1402
    Synonym: PENICILLINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:69 , SER A:70 , ASN A:170 , GLY A:236 , ALA A:237 , HOH A:537 , HOH A:555binding site for residue ACY A 301
2AC2SOFTWARESER A:87 , ILE A:88 , GLU A:202 , LYS A:203 , ASP A:275 , LYS A:277binding site for residue EDO A 302
3AC3SOFTWAREALA B:69 , SER B:70 , ASN B:170 , GLY B:236 , ALA B:237 , HOH B:520 , HOH B:546binding site for residue ACY B 301
4AC4SOFTWARESER B:87 , ILE B:88 , GLU B:202 , LYS B:203 , ASP B:275 , LYS B:277 , HOH B:567binding site for residue EDO B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GHX)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:166 -Pro A:167
2His B:166 -Pro B:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GHX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GHX)

(-) Exons   (0, 0)

(no "Exon" information available for 5GHX)

(-) 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:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.eeeeeeee.....eeee....eee...hhhhhhhhhhhhhh.hhhhh.ee..hhhhh.....hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ghx A  32 DFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFHPELNEVNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALNMN 293
                                    41        51     || 62        72        82||      94       104       114       124       134       144       154       164       174       184       194       204       214       224       234   ||  245      |256       266       276       286       
                                                    57|                      83|                                                                                                                                                     238|         252|                                       
                                                     59                       86                                                                                                                                                      240          254                                       


Chain B from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.eeeeeeee.....eeee....eee...hhhhhhhhhhhhhh.hhhhh.ee..hhhhh.....hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ghx B  31 DDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFHPELNEVNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 291
                                    40        50      ||61        71        81 ||     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    || 244       255       265       275       285      
                                                     57|                      83|                                                                                                                                                     238|         252|                                     
                                                      59                       86                                                                                                                                                      240          254
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5GHX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GHX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GHX)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BLAC_BACLI | P00808: 1i2s 1i2w 1mbl 1w7f 2blm 2wk0 2y91 3b3x 3ly3 3ly4 3m2j 3m2k 3sh7 3sh8 3sh9 3soi 4blm 4m3k 4n1h 4n92 4n9k 4n9l 5ghy 5ghz

(-) Related Entries Specified in the PDB File

5ghy 5ghz