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(-) Description

Title :  STRUCTURAL AND MECHANISTIC INSIGHTS INTO NDM-1 CATALYZED HYDROLYSIS OF CEPHALOSPORINS
 
Authors :  H. Feng, J. Ding, D. Zhu, X. Liu, X. Xu, Y. Zhang, S. Zang, D. -C. Wang, W. Li
Date :  14 Oct 14  (Deposition) - 19 Nov 14  (Release) - 19 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Ndm-1 Antibiotic Hydrolysis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Feng, J. Ding, D. Zhu, X. Liu, X. Xu, Y. Zhang, S. Zang, D. C. Wang, W. Li
Structural And Mechanistic Insights Into Ndm-1 Catalyzed Hydrolysis Of Cephalosporins.
J. Am. Chem. Soc. V. 136 14694 2014
PubMed-ID: 25268575  |  Reference-DOI: 10.1021/JA508388E

(-) Compounds

Molecule 1 - BETA-LACTAMASE NDM-1
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BLANDM-1
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573
    Synonym: NDM-1, METALLO-BETA-LACTAMASE NDM-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
13S02Ligand/Ion(2R,5S)-5-[(CARBAMOYLOXY)METHYL]-2-[(R)-CARBOXY{[(2Z)-2-(FURAN-2-YL)-2-(METHOXYIMINO)ACETYL]AMINO}METHYL]-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
13S02Ligand/Ion(2R,5S)-5-[(CARBAMOYLOXY)METHYL]-2-[(R)-CARBOXY{[(2Z)-2-(FURAN-2-YL)-2-(METHOXYIMINO)ACETYL]AMINO}METHYL]-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13S01Ligand/Ion(2R,5S)-5-[(CARBAMOYLOXY)METHYL]-2-[(R)-CARBOXY{[(2Z)-2-(FURAN-2-YL)-2-(METHOXYIMINO)ACETYL]AMINO}METHYL]-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
13S01Ligand/Ion(2R,5S)-5-[(CARBAMOYLOXY)METHYL]-2-[(R)-CARBOXY{[(2Z)-2-(FURAN-2-YL)-2-(METHOXYIMINO)ACETYL]AMINO}METHYL]-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:120 , HIS A:122 , HIS A:189 , 3S0 A:303 , HOH A:426BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREASP A:124 , CYS A:208 , HIS A:250 , 3S0 A:303 , HOH A:426BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREILE A:35 , LEU A:65 , TRP A:93 , HIS A:122 , GLN A:123 , ASP A:124 , GLU A:152 , HIS A:189 , CYS A:208 , LYS A:211 , GLY A:219 , ASN A:220 , HIS A:250 , ZN A:301 , ZN A:302 , HOH A:426 , HOH A:563 , THR B:34 , PRO B:68 , GLY B:69 , PHE B:70BINDING SITE FOR RESIDUE 3S0 A 303
4AC4SOFTWAREHIS B:120 , HIS B:122 , HIS B:189 , 3S0 B:303 , HOH B:419BINDING SITE FOR RESIDUE ZN B 301
5AC5SOFTWAREASP B:124 , CYS B:208 , HIS B:250 , 3S0 B:303 , HOH B:419BINDING SITE FOR RESIDUE ZN B 302
6AC6SOFTWARETHR A:34 , PHE A:70 , HOH A:529 , ILE B:35 , LEU B:65 , TRP B:93 , HIS B:122 , GLN B:123 , ASP B:124 , HIS B:189 , CYS B:208 , LYS B:211 , GLY B:219 , ASN B:220 , HIS B:250 , ZN B:301 , ZN B:302 , HOH B:419 , HOH B:592BINDING SITE FOR RESIDUE 3S0 B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RL0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RL0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RL0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RL0)

(-) Exons   (0, 0)

(no "Exon" information available for 4RL0)

(-) 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:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eeeeeee..eeeeeeeee...eeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eeeee....................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rl0 A  32 RPTIDQRFGDLVFRQLAPNVWQHTSYLDMFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                               ||   48        58        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
                              35|                      67|                                                                                                                                                                                                        
                               43                       70                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee..eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eeeeehhh.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rl0 B  32 RPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4RL0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RL0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RL0)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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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 4rl2 4rm5 4u4l 5a5z 5jqj 5k4k 5k4m 5k4n 5n0h 5n0i

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