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(-) Description

Title :  CRYSTAL STRUCTURE OF SERRATIA FONTICOLA SFH-I: GLYCEROL COMPLEX
 
Authors :  F. Fonseca, M. J. Saavedra, A. Correia, J. Spencer
Date :  03 Jan 11  (Deposition) - 13 Jul 11  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.37
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Metalloenzyme, Alpha-Beta, Metallo-Beta-Lactamase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Fonseca, E. H. C. Bromley, M. J. Saavedra, A. Correia, J. Spencer
Crystal Structure Of Serratia Fonticola Sfh-I: Activation O The Nucleophile In Mono-Zinc Metallo-Beta-Lactamases
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-26B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 3-234
    Gene: BLASFH-I, SFHI
    Organism Scientific: SERRATIA FONTICOLA
    Organism Taxid: 47917
    Strain: UTAD54

 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
1GOL2Ligand/IonGLYCEROL
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:118 , ASP A:120 , HIS A:196 , CYS A:221 , ASN A:233 , HIS A:263 , HOH A:281 , HOH A:283 , ZN A:2BINDING SITE FOR RESIDUE GOL A 1
2AC2SOFTWAREGOL A:1 , ASP A:120 , CYS A:221 , HIS A:263BINDING SITE FOR RESIDUE ZN A 2
3AC3SOFTWAREZN B:2 , HIS B:118 , ASP B:120 , HIS B:196 , CYS B:221 , ASN B:233 , HIS B:263 , HOH B:353 , HOH B:504BINDING SITE FOR RESIDUE GOL B 1
4AC4SOFTWAREGOL B:1 , ASP B:120 , CYS B:221 , HIS B:263BINDING SITE FOR RESIDUE ZN B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q6V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q6V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q6V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q6V)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q6V)

(-) 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
 aligned with Q9RMI1_SERFO | Q9RMI1 from UniProtKB/TrEMBL  Length:234

    Alignment length:228
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225        
        Q9RMI1_SERFO      6 NLTLTHFKGPLYIVEDKEYVQENSMVYIGTDGITIIGATWTPETAETLYKEIRKVSPLPINEVINTNYHTDRAGGNAYWKTLGAKIVATQMTYDLQKSQWGSIVNFTRQGNNKYPNLEKSLPDTVFPGDFNLQNGSIRAMYLGEAHTKDGIFVYFPAERVLYGNCILKENLGNMSFANRTEYPKTLEKLKGLIEQGELKVDSIIAGHDTPIHDVGLIDHYLTLLEKAP  233
               SCOP domains d3q6va_ A: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..eeeeee.....eeeeeee....eeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhhh............eee...eee....eeee...........eeee....eee.................hhhhhhhhhhhhhhhh......eee......ee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3q6v A   41 NLTLTHFKGPLYIVEDKEYVQENSMVYIGTDGITIIGATWTPETAETLYKEIRKVSPLPINEVINTNYHTDRAGGNAYWKTLGAKIVATQMTYDLQKSQWGSIVNFTRQGNNKYPNLEKSLPDTVFPGDFNLQNGSIRAMYLGEAHTKDGIFVYFPAERVLYGNCILKENLGNMSFANRTEYPKTLEKLKGLIEQGELKVDSIIAGHDTPIHDVGLIDHYLTLLEKAP  305
                                    50        67        77        87        97  ||   109       119       129 ||    140       150       160       170       180       190       200    || 216       226|      240       250    |||256       266||     297        
                                             59|                              100| 106|                    131|                                                                     205| ||        226|                    254A|||          267|                
                                              67                               102  108                     133                                                                      209 ||         231                     254B||           289                
                                                                                                                                                                                       211|                                  254C|                              
                                                                                                                                                                                        215                                   254D                              


Chain B from PDB  Type:PROTEIN  Length:228
 aligned with Q9RMI1_SERFO | Q9RMI1 from UniProtKB/TrEMBL  Length:234

    Alignment length:228
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225        
        Q9RMI1_SERFO      6 NLTLTHFKGPLYIVEDKEYVQENSMVYIGTDGITIIGATWTPETAETLYKEIRKVSPLPINEVINTNYHTDRAGGNAYWKTLGAKIVATQMTYDLQKSQWGSIVNFTRQGNNKYPNLEKSLPDTVFPGDFNLQNGSIRAMYLGEAHTKDGIFVYFPAERVLYGNCILKENLGNMSFANRTEYPKTLEKLKGLIEQGELKVDSIIAGHDTPIHDVGLIDHYLTLLEKAP  233
               SCOP domains d3q6vb_ B: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..eeeeee.....eeeeeee....eeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhhh............eee...eeehhhheeee...........eeee....eee.................hhhhhhhhhhhhhhhh......eee......ee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3q6v B   41 NLTLTHFKGPLYIVEDKEYVQENSMVYIGTDGITIIGATWTPETAETLYKEIRKVSPLPINEVINTNYHTDRAGGNAYWKTLGAKIVATQMTYDLQKSQWGSIVNFTRQGNNKYPNLEKSLPDTVFPGDFNLQNGSIRAMYLGEAHTKDGIFVYFPAERVLYGNCILKENLGNMSFANRTEYPKTLEKLKGLIEQGELKVDSIIAGHDTPIHDVGLIDHYLTLLEKAP  305
                                    50        67        77        87        97  ||   109       119       129 ||    140       150       160       170       180       190       200    || 216       226|      240       250    |||256       266||     297        
                                             59|                              100| 106|                    131|                                                                     205| ||        226|                    254A|||          267|                
                                              67                               102  108                     133                                                                      209 ||         231                     254B||           289                
                                                                                                                                                                                       211|                                  254C|                              
                                                                                                                                                                                        215                                   254D
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q6V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3Q6V)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9RMI1_SERFO | Q9RMI1)
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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0017001    antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    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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        Q9RMI1_SERFO | Q9RMI1: 3sd9 5ew0

(-) Related Entries Specified in the PDB File

3q42 STRUCTURE OF UNLIGANDED ENZYME