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(-) Description

Title :  DIRECTED EVOLUTIONARY CHANGES IN MBL SUPER FAMILY - NDM-1 ROUND 10 CRYSTAL-4
 
Authors :  N. -S. Hong, C. J. Jackson, P. D. Carr
Date :  20 May 16  (Deposition) - 26 Apr 17  (Release) - 26 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym. Unit :  A,K
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  K  (1x)
Keywords :  Phosphatase, Directed Evolution, Mbl Super Family, Ndm-1, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Baier, N. -S. Hong, G. Yang, P. D. Carr, C. Jackson, N. Tokuriki
Enzyme Evolvability Is Contingent On The Initial Sequence Background
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METALLO-BETA-LACTAMASE TYPE 2
    Chains: A, K
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 29-270
    Gene: BLANDM-1
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573
    Synonym: B2 METALLO-BETA-LACTAMASE,BETA-LACTAMASE TYPE II,METALLO- BETA-LACTAMASE NDM-1,METALLO-BETA-LACTAMASE TYPE II,NEW DELHI METALLO-BETA-LACTAMASE-1,NDM-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AK
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  K

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric Unit (5, 16)
No.NameCountTypeFull Name
1MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2MG4Ligand/IonMAGNESIUM ION
3NPO2Ligand/IonP-NITROPHENOL
4SV74Ligand/IonPHENYLPHOSPHONIC ACID
5ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3NPO1Ligand/IonP-NITROPHENOL
4SV72Ligand/IonPHENYLPHOSPHONIC ACID
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3NPO1Ligand/IonP-NITROPHENOL
4SV72Ligand/IonPHENYLPHOSPHONIC ACID
5ZN-1Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:120 , HIS A:122 , HIS A:189 , SV7 A:307binding site for residue ZN A 301
02AC2SOFTWAREASP A:124 , CYS A:208 , HIS A:250 , SV7 A:307binding site for residue ZN A 302
03AC3SOFTWAREVAL A:73 , ASN A:176 , PHE A:177 , GLY A:178 , ARG A:211 , LYS A:216 , SER A:217 , HIS A:250binding site for residue MES A 303
04AC4SOFTWAREGLU A:152 , GLU A:223 , GLU A:227 , HOH A:542binding site for residue MG A 304
05AC5SOFTWAREASP A:95 , HOH A:434 , HOH A:437 , HOH A:537 , HOH A:618 , HOH K:512binding site for residue MG A 305
06AC6SOFTWAREGLN A:53 , TRP A:59 , TYR A:64 , ARG A:81 , GLU A:108 , HOH A:404 , HOH A:550binding site for residue SV7 A 306
07AC7SOFTWARELEU A:65 , HIS A:120 , HIS A:122 , ASP A:124 , HIS A:189 , HIS A:250 , ZN A:301 , ZN A:302 , HOH A:422binding site for residue SV7 A 307
08AC8SOFTWAREALA A:99 , LEU A:102 , ALA A:131 , ALA A:134 , ALA A:135 , HOH A:402 , ALA K:96 , ALA K:99 , NPO K:301binding site for residue NPO A 308
09AC9SOFTWAREALA A:96 , NPO A:308 , ALA K:99 , LEU K:102 , ALA K:131 , ALA K:134 , ALA K:135 , HOH K:405binding site for residue NPO K 301
10AD1SOFTWAREHIS K:120 , HIS K:122 , HIS K:189 , SV7 K:308binding site for residue ZN K 302
11AD2SOFTWAREASP K:124 , CYS K:208 , HIS K:250 , SV7 K:308binding site for residue ZN K 303
12AD3SOFTWAREARG K:85 , ASN K:176 , PHE K:177 , GLY K:178 , ARG K:211 , LYS K:216 , SER K:217 , HOH K:542binding site for residue MES K 304
13AD4SOFTWAREGLU K:152 , GLU K:223 , GLU K:227 , HOH K:403binding site for residue MG K 305
14AD5SOFTWAREHOH A:510 , ASP K:95 , HOH K:455 , HOH K:462 , HOH K:517 , HOH K:593binding site for residue MG K 306
15AD6SOFTWAREARG K:52 , GLN K:53 , TRP K:59 , TYR K:64 , ARG K:81 , GLU K:108 , HOH K:409binding site for residue SV7 K 307
16AD7SOFTWAREHIS K:120 , HIS K:122 , ASP K:124 , HIS K:189 , HIS K:250 , ZN K:302 , ZN K:303 , HOH K:408 , HOH K:446binding site for residue SV7 K 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K4K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5K4K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K4K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K4K)

(-) Exons   (0, 0)

(no "Exon" information available for 5K4K)

(-) 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:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee..eeeeeeeee.....eeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eee.hhhh.................hhhhhhhhhhhhh....eee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k4k A  43 DQRFGDPVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLMVDTAGTDAQTAQILKWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPREGVVAAQHSLTFAATGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIRDSKAKSLGNLDEADTEHYAASVRAFGAAFPKASMIVMSHFAPDSRAAITHTARMADKLR 270
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262        


Chain K from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee..eeeeeeeee.....eeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhh......eee........hhhhh.....eeee...........eeee....eee.hhhh.................hhhhhhhhhhhhh....eee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k4k K  43 DQRFGDPVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLMVDTAGTDAQTAQILKWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPREGVVAAQHSLTFAATGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIRDSKAKSLGNLDEADTEHYAASVRAFGAAFPKASMIVMSHFAPDSRAAITHTARMADKLR 270
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262
   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  (0, 0)

(no "SCOP Domain" information available for 5K4K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K4K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K4K)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BLAN1_KLEPN | C7C422: 3pg4 3q6x 3rkj 3rkk 3sbl 3sfp 3spu 3srx 3zr9 4exs 4exy 4ey2 4eyb 4eyf 4eyl 4gyq 4gyu 4h0d 4hky 4hl1 4hl2 4ram 4raw 4rbs 4rl0 4rl2 4rm5 4u4l 5a5z 5jqj 5k4m 5k4n 5n0h 5n0i

(-) Related Entries Specified in the PDB File

5jqj 5k4m 5k4n