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(-) Description

Title :  X-RAY CRYSTALLOGRAPHIC STRUCTURE OF CTX-M-9 BETA-LACTAMASE COMPLEXED WITH NAFCININ-LIKE BORONIC ACID INHIBITOR
 
Authors :  Y. Chen, B. Shoichet, R. Bonnet
Date :  21 Jan 05  (Deposition) - 26 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ctx-M, Beta-Lactamase, Transition State, Acylation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Chen, B. Shoichet, R. Bonnet
Structure, Function, And Inhibition Along The Reaction Coordinate Of Ctx-M Beta-Lactamases.
J. Am. Chem. Soc. V. 127 5423 2005
PubMed-ID: 15826180  |  Reference-DOI: 10.1021/JA042850A
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE CTX-M-9
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-9A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CTX-M
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NBF2Ligand/Ion[(2-ETHOXY-1-NAPHTHOYL)AMINO]METHYLBORONIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NBF1Ligand/Ion[(2-ETHOXY-1-NAPHTHOYL)AMINO]METHYLBORONIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NBF1Ligand/Ion[(2-ETHOXY-1-NAPHTHOYL)AMINO]METHYLBORONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:69 , SER A:70 , ASN A:104 , SER A:130 , ASN A:132 , PRO A:167 , ASN A:170 , GLY A:236 , SER A:237 , ASP A:240 , HOH A:2001BINDING SITE FOR RESIDUE NBF A 1001
2AC2SOFTWARECYS B:69 , SER B:70 , ASN B:104 , SER B:130 , ASN B:132 , PRO B:167 , ASN B:170 , GLY B:236 , SER B:237 , ASP B:240 , HOH B:2002BINDING SITE FOR RESIDUE NBF B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YMS)

(-) 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 1YMS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YMS)

(-) Exons   (0, 0)

(no "Exon" information available for 1YMS)

(-) 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:263
 aligned with Q9L5C8_ECOLX | Q9L5C8 from UniProtKB/TrEMBL  Length:291

    Alignment length:263
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288   
         Q9L5C8_ECOLX    29 QTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 291
               SCOP domains d1ymsa_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1ymsA00 A:25-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhh...hhhh.eeeehhhhh.....hhhhhh.eeeehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yms A  25 QTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 290
                                    34        44        54  ||    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287   
                                                           57|                                                                                                                                                                                238|         252|                                    
                                                            59                                                                                                                                                                                 240          254                                    


Chain B from PDB  Type:PROTEIN  Length:261
 aligned with Q9L5C8_ECOLX | Q9L5C8 from UniProtKB/TrEMBL  Length:291

    Alignment length:261
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 
         Q9L5C8_ECOLX    31 SAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 291
               SCOP domains d1ymsb_ B: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1ymsB00 B:27-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                              CATH domains
           Pfam domains (1) ------------------------Beta-lactamase2-1ymsB01 B:51-263                                                                                                                                                                                  --------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------Beta-lactamase2-1ymsB02 B:51-263                                                                                                                                                                                  --------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhh....hhhh.eeeehhhhh.....hhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yms B  27 SAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 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 
                                                         57|                                                                                                                                                                                238|         252|                                    
                                                          59                                                                                                                                                                                 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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Beta-lactamase (210)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9L5C8_ECOLX | Q9L5C8)
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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 Related Entries

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

UniProtKB/TrEMBL
        Q9L5C8_ECOLX | Q9L5C8: 1ylj 1ym1 1ymx 2p74 3g2y 3g2z 3g30 3g31 3g32 3g34 3g35 3hlw 3hre 3huo 3hvf 3q07 3q1f 4dds 4ddy 4de0 4de1 4de2 4de3 4len 5ujo

(-) Related Entries Specified in the PDB File

1ylj 1yly 1ym1