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(-) Description

Title :  ANCESTRAL PNCA (LAST COMMON ANCESTORS OF GRAM-POSITIVE AND GRAM-NEGATIVE BACTERIA) BETA-LACTAMASE CLASS A
 
Authors :  J. A. Gavira, V. A. Risso, J. M. Sanchez-Ruiz
Date :  19 Sep 13  (Deposition) - 16 Apr 14  (Release) - 28 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Antibiotic Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. A. Risso, J. A. Gavira, E. A. Gaucher, J. M. Sanchez-Ruiz
Phenotypic Comparisons Of Consensus Variants Versus Laboratory Resurrections Of Precambrian Proteins.
Proteins V. 82 887 2014
PubMed-ID: 24710963  |  Reference-DOI: 10.1002/PROT.24575
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: RESURRECTED SEQUENCE, ANCESTRAL RECONSTRUCTED

 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  (6, 29)

Asymmetric Unit (6, 29)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4NA2Ligand/IonSODIUM ION
5PEG21Ligand/IonDI(HYDROXYETHYL)ETHER
6PG42Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (4, 16)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4NA-1Ligand/IonSODIUM ION
5PEG13Ligand/IonDI(HYDROXYETHYL)ETHER
6PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3GOL-1Ligand/IonGLYCEROL
4NA-1Ligand/IonSODIUM ION
5PEG8Ligand/IonDI(HYDROXYETHYL)ETHER
6PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:83 , GLN A:86 , LYS A:88 , PHE A:151 , LYS A:215BINDING SITE FOR RESIDUE PG4 A 291
02AC2SOFTWAREASP A:163 , GLU A:205 , GLN A:206 , HOH A:2136BINDING SITE FOR RESIDUE PEG A 292
03AC3SOFTWAREARG A:204 , ALA A:272 , GLU A:273BINDING SITE FOR RESIDUE NA A 293
04AC4SOFTWAREILE A:155 , ASP A:157 , ALA A:185 , ALA A:188 , THR A:189 , HOH A:2119 , HOH A:2206BINDING SITE FOR RESIDUE PEG A 294
05AC5SOFTWAREPRO A:107 , LYS A:111 , HOH A:2096 , HOH A:2098BINDING SITE FOR RESIDUE PEG A 295
06AC6SOFTWAREARG A:222 , LEU A:225 , PRO A:226 , TRP A:229BINDING SITE FOR RESIDUE ACT A 296
07AC7SOFTWAREARG A:39 , SER A:40 , GLU A:281 , PEG A:298BINDING SITE FOR RESIDUE PEG A 297
08AC8SOFTWAREALA A:274 , PEG A:297BINDING SITE FOR RESIDUE PEG A 298
09AC9SOFTWAREARG A:43 , ARG A:65 , PRO A:174 , GLY A:175 , ASP A:176 , PRO A:177 , HOH A:2020 , HOH A:2209BINDING SITE FOR RESIDUE PEG A 299
10BC1SOFTWARESER A:154 , LYS A:192 , GLN A:269 , HOH A:2145BINDING SITE FOR RESIDUE PEG A 300
11BC2SOFTWAREARG A:56 , ILE A:57 , ALA A:58 , ARG A:184 , NA A:308 , HOH A:2139BINDING SITE FOR RESIDUE PEG A 301
12BC3SOFTWAREGLY A:87 , ARG A:90 , ARG A:93 , HOH A:2065BINDING SITE FOR RESIDUE PEG A 302
13BC4SOFTWAREARG A:94 , GLY A:116 , GLU A:121 , GLU B:31 , GLU B:35BINDING SITE FOR RESIDUE PEG A 303
14BC5SOFTWAREARG A:93 , ILE A:95 , LEU A:137 , ALA A:141 , ALA A:227 , ARG A:230 , HOH A:2112BINDING SITE FOR RESIDUE PEG A 304
15BC6SOFTWARELYS A:219BINDING SITE FOR RESIDUE PEG A 305
16BC7SOFTWAREPRO A:167BINDING SITE FOR RESIDUE GOL A 306
17BC8SOFTWARESER A:70 , SER A:130 , ASN A:132 , THR A:235 , GLY A:236 , THR A:237 , HOH A:2052BINDING SITE FOR RESIDUE PEG A 307
18BC9SOFTWAREARG A:56 , ARG A:184 , PEG A:301BINDING SITE FOR RESIDUE NA A 308
19CC1SOFTWAREHOH A:2200 , VAL B:48 , ARG B:56 , ILE B:57 , ARG B:184 , ALA B:188 , HOH B:2069 , HOH B:2093BINDING SITE FOR RESIDUE PEG B 291
20CC2SOFTWAREALA A:257 , ARG B:65 , HOH B:2065BINDING SITE FOR RESIDUE CL B 292
21CC3SOFTWARESER B:70 , TYR B:105 , SER B:130 , ASN B:132 , THR B:235 , GLY B:236 , THR B:237BINDING SITE FOR RESIDUE PEG B 293
22CC4SOFTWAREGLU B:140 , TRP B:165 , HOH B:2041BINDING SITE FOR RESIDUE PEG B 294
23CC5SOFTWAREASP B:163 , ARG B:164 , TRP B:165 , GLU B:168 , HOH B:2060BINDING SITE FOR RESIDUE PEG B 295
24CC6SOFTWARELEU B:212 , ASN B:214 , LYS B:215 , ASP B:218BINDING SITE FOR RESIDUE PEG B 296
25CC7SOFTWARELYS A:111 , HIS A:112 , LYS B:38BINDING SITE FOR RESIDUE PEG B 297
26CC8SOFTWARELEU B:142 , ALA B:147 , SER B:154 , HOH B:2023BINDING SITE FOR RESIDUE PEG B 298
27CC9SOFTWAREASP B:85 , LYS B:111 , SER B:203 , GLN B:206BINDING SITE FOR RESIDUE PEG B 299
28DC1SOFTWARETHR A:53 , ARG A:55 , ARG B:161BINDING SITE FOR RESIDUE ACT B 300
29DC2SOFTWARELYS B:219BINDING SITE FOR RESIDUE PG4 B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C6Y)

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C6Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C6Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4C6Y)

(-) 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhhhh.......ee..hhhhh.....hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c6y A  26 AAALSEQLAELEKRSGGRLGVAVLDTATGRRIAYRGDERFPMCSTFKALLAAAVLAQVDQGKERLDRRITYSKADLVDYSPVTEKHVGGGMTVAELCEAAITYSDNTAANLLLEALGGPAALTAFLRSIGDEVTRLDRWEPELNEALPGDPRDTTTPRAMAATLRKLLLGDALSPASREQLVDWLLANKTGDKRLRAGLPADWRVGDKTGTGGHGTTNDIAVIWPPNRAPIVVAVYYTESQADAEARDAVIAEVGRLVAEAF 290
                                    35        45        55  ||    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236 ||    247    || 258       268       278       288  
                                                           58|                                                                                                                                                                               238|         252|                                    
                                                            60                                                                                                                                                                                240          254                                    


Chain B from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhhhh.......ee..hhhhh.....hhhhh....eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh......eeeeeee...eeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c6y B  27 AALSEQLAELEKRSGGRLGVAVLDTATGRRIAYRGDERFPMCSTFKALLAAAVLAQVDQGKERLDRRITYSKADLVDYSPVTEKHVGGGMTVAELCEAAITYSDNTAANLLLEALGGPAALTAFLRSIGDEVTRLDRWEPELNEALPGDPRDTTTPRAMAATLRKLLLGDALSPASREQLVDWLLANKTGDKRLRAGLPADWRVGDKTGTGGHGTTNDIAVIWPPNRAPIVVAVYYTESQADAEARDAVIAEVGRLVAEAF 290
                                    36        46        56 ||     67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237||     248   ||  259       269       279       289 
                                                          58|                                                                                                                                                                               238|         252|                                    
                                                           60                                                                                                                                                                                240          254
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 4C6Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C6Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C6Y)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4C6Y)

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4c75 CONSENSUS (ALL-CON) BETA-LACTAMASE CLASS A