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(-) Description

Title :  COVALENT ACYL ENZYME COMPLEX OF THE R61 DD-PEPTIDASE WITH A HIGHLY SPECIFIC CEPHALOSPORIN
 
Authors :  N. R. Silvaggi, H. R. Josephine, R. F. Pratt, J. A. Kelly
Date :  01 Jul 03  (Deposition) - 13 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Lactam, Antibiotics, Penicillin Binding Protein, Enzyme, Peptidoglycan, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. R. Silvaggi, H. R. Josephine, A. P. Kuzin, R. Nagarajan, R. F. Pratt, J. A. Kelly
Crystal Structures Of Complexes Between The R61 Dd-Peptidas And Peptidoglycan-Mimetic Beta-Lactams: A Non-Covalent Complex With A "Perfect Penicillin"
J. Mol. Biol. V. 345 521 2005
PubMed-ID: 15581896  |  Reference-DOI: 10.1016/J.JMB.2004.10.076
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
    Chains: A
    EC Number: 3.4.16.4
    Fragment: DD-PEPTIDASE
    Organism Scientific: STREPTOMYCES SP.
    Organism Taxid: 31952
    Strain: R61
    Synonym: DD-PEPTIDASE, DD-CARBOXYPEPTIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2H2A1Ligand/Ion(6R,7R)-3-[(ACETYLOXY)METHYL]-7-{[(6S)-6-(GLYCYLAMINO)-7-OXIDO-7-OXOHEPTANOYL]AMINO}-8-OXO-5-THIA-1-AZABICYCLO[4.2.0]OCTANE-2-CARBOXYLATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:62 , ASP A:98 , ARG A:99 , PHE A:120 , THR A:123 , TYR A:159 , ASN A:161 , LEU A:214 , THR A:299 , GLY A:300 , THR A:301 , GLN A:303 , SER A:326 , ASN A:327 , GOL A:500 , HOH A:2008 , HOH A:2012 , HOH A:2041 , HOH A:2244 , HOH A:2367BINDING SITE FOR RESIDUE H2A A 400
2AC2SOFTWAREASP A:97 , ARG A:99 , PRO A:153 , TYR A:306 , ASN A:327 , VAL A:329 , H2A A:400 , HOH A:2105 , HOH A:2135BINDING SITE FOR RESIDUE GOL A 500
3AC3SOFTWAREVAL A:204 , ILE A:205 , GLY A:207 , HIS A:209 , HOH A:2028 , HOH A:2224 , HOH A:2257BINDING SITE FOR RESIDUE GOL A 501

(-) 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 1PW8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PW8)

(-) Exons   (0, 0)

(no "Exon" information available for 1PW8)

(-) 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:345
 aligned with DAC_STRSR | P15555 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:345
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373     
            DAC_STRSR    34 LPAPDDTGLQAVLHTALSQGAPGAMVRVDDNGTIHQLSEGVADRATGRAITTTDRFRVGSVTKSFSAVVLLQLVDEGKLDLDASVNTYLPGLLPDDRITVRQVMSHRSGLYDYTNDMFAQTVPGFESVRNKVFSYQDLITLSLKHGVTNAPGAAYSYSNTNFVVAGMLIEKLTGHSVATEYQNRIFTPLNLTDTFYVHPDTVIPGTHANGYLTPDEAGGALVDSTEQTVSWAQSAGAVISSTQDLDTFFSALMSGQLMSAAQLAQMQQWTTVNSTQGYGLGLRRRDLSCGISVYGHTGTVQGYYTYAFASKDGKRSVTALANTSNNVNVLNTMARTLESAFCGKP 378
               SCOP domains d1pw8a_ A: D-ala carboxypeptidase/transpeptidase                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1pw8A00 A:3-347 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains Beta-lactamase-1pw8A01 A:3-342                                                                                                                                                                                                                                                                                                                      ----- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee...............ee...hhhhhhhhhhhhhhhh.......hhhhhh.........hhhhhhh.......hhhhhh.hhhhhhhhhh....hhhhhhhhhhh.............hhhhhhhhhhhhhhhhh.hhhhhhhhhh.........................ee.........ee........hhhhh..eehhhhhhhhhhhhhh....hhhhhhhhh..eeee..eee....eeee.....eeeeeeeee..eeeeeee.....eeeeeee.ee.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pw8 A   3 LPAPDDTGLQAVLHTALSQGAPGAMVRVDDNGTIHQLSEGVADRATGRAITTTDRFRVGSVTKSFSAVVLLQLVDEGKLDLDASVNTYLPGLLPDDRITVRQVMSHRSGLYDYTNDMFAQTVPGFESVRNKVFSYQDLITLSLKHGVTNAPGAAYSYSNTNFVVAGMLIEKLTGHSVATEYQNRIFTPLNLTDTFYVHPDTVIPGTHANGYLTPDEAGGALVDSTEQTVSWAQSAGAVISSTQDLDTFFSALMSGQLMSAAQLAQMQQWTTVNSTQGYGLGLRRRDLSCGISVYGHTGTVQGYYTYAFASKDGKRSVTALANTSNNVNVLNTMARTLESAFCGKP 347
                                    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       272       282       292       302       312       322       332       342
   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, 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  (1, 1)

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

(-) 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 | P15555: 1cef 1ceg 1hvb 1ikg 1iki 1mpl 1pw1 1pwc 1pwd 1pwg 1scw 1sde 1yqs 2pte 3pte

(-) Related Entries Specified in the PDB File

1ikg MICHAELIS COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT
1iki COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH THE PRODUCTS OF A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT
1mpl CRYSTAL STRUCTURE OF PHOSPHONATE-INHIBITED D-ALA-D-ALA PEPTIDASE REVEALS AN ANALOG OF A TETRAHEDRAL TRANSITION STATE