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(-) Description

Title :  CEFOTAXIME COMPLEXED WITH THE STREPTOMYCES R61 DD-PEPTIDASE
 
Authors :  J. R. Knox, A. P. Kuzin
Date :  12 Jan 95  (Deposition) - 14 Oct 96  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym./Biol. Unit :  A
Keywords :  D-Amino Acid Peptidase, Penicillin Target, Hydrolase-Transpeptidase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. P. Kuzin, H. Liu, J. A. Kelly, J. R. Knox
Binding Of Cephalothin And Cefotaxime To D-Ala-D-Ala-Peptidase Reveals A Functional Basis Of A Natural Mutation In A Low-Affinity Penicillin-Binding Protein And In Extended-Spectrum Beta-Lactamases.
Biochemistry V. 34 9532 1995
PubMed-ID: 7626623  |  Reference-DOI: 10.1021/BI00029A030
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-ALANYL-D-ALANINE CARBOXYPEPTIDASE TRANSPEPTIDASE
    ChainsA
    EC Number3.4.16.4
    Organism ScientificSTREPTOMYCES SP.
    Organism Taxid31952
    StrainR61
    SynonymPENICILLIN TARGET

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CEF1Ligand/IonCEFOTAXIME GROUP

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:62 , ASP A:98 , ARG A:99 , TYR A:159 , ASN A:161 , TRP A:233 , THR A:299 , THR A:301 , HOH A:496 , HOH A:509BINDING SITE FOR RESIDUE CEF A 400
2ACTUNKNOWNSER A:62 , LYS A:65 , THR A:116 , TYR A:159 , SER A:160 , ASN A:161 , HIS A:298 , THR A:299 , GLY A:300 , THR A:301THOSE FOR S. R61 ARE LISTED BELOW.

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:291 -A:344

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:200 -Pro A:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1CEF)

(-) 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:347
 aligned with DAC_STRSR | P15555 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:347
                                    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       301       311       321       331       341       351       361       371       
            DAC_STRSR    32 ADLPAPDDTGLQAVLHTALSQGAPGAMVRVDDNGTIHQLSEGVADRATGRAITTTDRFRVGSVTKSFSAVVLLQLVDEGKLDLDASVNTYLPGLLPDDRITVRQVMSHRSGLYDYTNDMFAQTVPGFESVRNKVFSYQDLITLSLKHGVTNAPGAAYSYSNTNFVVAGMLIEKLTGHSVATEYQNRIFTPLNLTDTFYVHPDTVIPGTHANGYLTPDEAGGALVDSTEQTVSWAQSAGAVISSTQDLDTFFSALMSGQLMSAAQLAQMQQWTTVNSTQGYGLGLRRRDLSCGISVYGHTGTVQGYYTYAFASKDGKRSVTALANTSNNVNVLNTMARTLESAFCGKP 378
               SCOP domains d1cefa_ A: D-ala carboxypeptidase/transpeptidase                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1cefA00 A:1-347 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh...eeeeeeee..eeeeeeeeeee...eee......eeehhhhhhhhhhhhhhhhhh........hhhh...........hhhhhh.......hhhhh...hhhhhhhhh.....hhhhhhhhhh..............hhhhhhhhhhhhhhh...hhhhhhhhhhhhh....eee.............eeee........eee........hhh..eee.hhhhhhhhhhhh......hhhhhhh...eeee..eeee..eeeee....eeeeeeeeee..eeeeeeee....eeeeeee.ee..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cef A   1 ADLPAPDDTGLQAVLHTALSQGAPGAMVRVDDNGTIHQLSEGVADRATGRAITTTDRFRVGSVTKSFSAVVLLQLVDEGKLDLDASVNTYLPGLLPDDRITVRQVMSHRSGLYDYTNDMFAQTVPGFESVRNKVFSYQDLITLSLKHGVTNAPGAAYSYSNTNFVVAGMLIEKLTGHSVATEYQNRIFTPLNLTDTFYVHPDTVIPGTHANGYLTPDEAGGALVDSTEQTVSWAQSAGAVISSTQDLDTFFSALMSGQLMSAAQLAQMQQWTTVNSTQGYGLGLRRRDLSCGISVYGHTGTVQGYYTYAFASKDGKRSVTALANTSNNVNVLNTMARTLESAFCGKP 347
                                    10        20        30        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       300       310       320       330       340       

   Legend:   → Mismatch (orange background)
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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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DAC_STRSR | P15555)
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
        DAC_STRSR | P155551ceg 1hvb 1ikg 1iki 1mpl 1pw1 1pw8 1pwc 1pwd 1pwg 1scw 1sde 1yqs 2pte 3pte

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1CEF)