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(-) Description

Title :  R248L MUTANT OF STREPTOMYCES K15 DD-TRANSPEPTIDASE
 
Authors :  E. Fonze, P. Charlier
Date :  10 Apr 00  (Deposition) - 03 May 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Penicillin-Binding, Dd-Transpeptidase, Serine Peptidase, Beta- Lactamase, Hydrolase Carboxypeptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Fonze, N. Rhazi, M. Nguyen-Disteche, P. Charlier
Dd-Transpeptidase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DD-TRANSPEPTIDASE
    Chains: A
    EC Number: 3.4.16.4
    Engineered: YES
    Expression System: STREPTOMYCES LIVIDANS TK24
    Expression System Strain: TK24
    Expression System Taxid: 457428
    Mutation: YES
    Organism Scientific: STREPTOMYCES SP.
    Organism Taxid: 1958
    Strain: K15
    Synonym: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE, DD-PEPTIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1ESI)

(-) Sites  (0, 0)

(no "Site" information available for 1ESI)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ESI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ESI)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ESI)

(-) Sequences/Alignments

Asymmetric/Biological 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:260
 aligned with DACX_STRSK | P39042 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:260
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
           DACX_STRSK    32 KPTIAAVGGYAMNNGTGTTLYTKAADTRRSTGSTTKIMTAKVVLAQSNLNLDAKVTIQKAYSDYVVANKPSQAHLIVGDKVTVRQLLYGLMLPSGCDAAYALADKYGSGSQAAARVKSFIGKMNTAATNLGLHNTHFDSFDGIGNGANYSTPRHLTKIASSAMKNSTFRTVVKTKAYTAKTVTKTGSIRTMDTWKNTNGLLSSYSGAIGVKTGSGPEAKYCLVFAATRGGKTVIGTVLASTSIPARESDATKIMNYGFAL 291
               SCOP domains d1esia_ A: D-ala carboxypeptidase/transpeptidase                                                                                                                                                                                                                     SCOP domains
               CATH domains 1esiA00 A:3-262 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.....eeeee.....ee.hhhhhhhhhhhhhhh.......eee.hhhhhhhhhhhh..........eeehhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..................eehhhhhhhhhhhhh.hhhhhhhhh..ee..eee.....eee...ee...hhhhhh..eeeeeeeee...eeeeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1esi A   3 KPTIAAVGGYAMNNGTGTTLYTKAADTRRSTGSTTKIMTAKVVLAQSNLNLDAKVTIQKAYSDYVVANNASQAHLIVGDKVTVRQLLYGLMLPSGCDAAYALADKYGSGSTRAARVKSFIGKMNTAATNLGLHNTHFDSFDGIGNGANYSTPRDLTKIASSAMKNSTFRTVVKTKAYTAKTVTKTGSIRTMDTWKNTNGLLSSYSGAIGVKTGSGPEAKYCLVFAATRGGKTVIGTVLASTSIPALESDATKIMNYGFAL 262
                                    12        22        32        42        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)
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    → 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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ESI)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DACX_STRSK | P39042)
molecular function
    GO:0004180    carboxypeptidase activity    Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0009002    serine-type D-Ala-D-Ala carboxypeptidase activity    Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
biological process
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DACX_STRSK | P39042: 1es2 1es3 1es4 1es5 1j9m 1skf

(-) Related Entries Specified in the PDB File

1eqs K38H MUTANT OF STREPTOMYCES K15 DD-TRANSPEPTIDASE
1es2 S96A MUTANT OF STREPTOMYCES K15 DD-TRANSPEPTIDASE
1es3 C98A MUTANT OF STREPTOMYCES K15 DD-TRANSPEPTIDASE
1es4 C98N MUTANT OF STREPTOMYCES K15 DD-TRANSPEPTIDASE
1es5 S216A MUTANT OF STREPTOMYCES K15 DD-TRANSPEPTIDASE
1skf 1SKF CONTAINS THE WILD TYPE PROTEIN.