Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AN OUTER MEMBRANE-ANCHORED ENDOLYTIC PEPTIDOGLYCAN LYTIC TRANSGLYCOSYLASE (MLTE) FROM ESCHERICHIA COLI
 
Authors :  C. Artola-Recolons, C. Carrasco-Lopez, L. I. Llarrull, M. Kumarasiri E. Lastochkin, I. Martinez-Ilarduya, K. Meindl, I. Uson, S. Mobasher J. A. Hermoso
Date :  08 Feb 11  (Deposition) - 13 Apr 11  (Release) - 13 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lyase, Cell Wall Biogenesis/Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Artola-Recolons, C. Carrasco-Lopez, L. I. Llarrull, M. Kumarasiri, E. Lastochkin, I. Martinez De Ilarduya, K. Meindl, I. Uson, S. Mobashery, J. A. Hermoso
High-Resolution Crystal Structure Of Mlte, An Outer Membrane-Anchored Endolytic Peptidoglycan Lytic Transglycosylase From Escherichia Coli.
Biochemistry V. 50 2384 2011
PubMed-ID: 21341761  |  Reference-DOI: 10.1021/BI200085Y

(-) Compounds

Molecule 1 - ENDO-TYPE MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE A
    Chains: A, B
    EC Number: 4.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Expression System Vector: PET-24A
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 19-203
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: PEPTIDOGLYCAN LYTIC ENDOTRANSGLYCOSYLASE

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2Y8P)

(-) Sites  (0, 0)

(no "Site" information available for 2Y8P)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y8P)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:24 -Pro A:25
2Asn B:24 -Pro B:25

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y8P)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSGLYCOSYLASEPS00922 Prokaryotic transglycosylases signature.EMTA_ECOLI60-88
 		  2A:60-88
B:60-88
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSGLYCOSYLASEPS00922 Prokaryotic transglycosylases signature.EMTA_ECOLI60-88
 		  1A:60-88
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSGLYCOSYLASEPS00922 Prokaryotic transglycosylases signature.EMTA_ECOLI60-88
 		  1-
B:60-88

(-) Exons   (0, 0)

(no "Exon" information available for 2Y8P)

(-) 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:190
 aligned with EMTA_ECOLI | P0C960 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:190
                                                                                                                                                                                                                  203     
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198    |    -
           EMTA_ECOLI    19 KHDYTNPPWNAKVPVQRAMQWMPISQKAGAAWGVDPQLITAIIAIESGGNPNAVSKSNAIGLMQLKASTSGRDVYRRMGWSGEPTTSELKNPERNISMGAAYLNILETGPLAGIEDPKVLQYALVVSYANGAGALLRTFSSDRKKAISKINDLDADEFLEHVARNHPAPQAPRYIYKLEQALDAM-----   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....................hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------TRANSGLYCOSYLASE  PDB: A:60-8------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y8p A  19 KHDYTNPPWNAKVPVQRAMQWMPISQKAGAAWGVDPQLITAIIAIESGGNPNAVSKSNAIGLMQLKASTSGRDVYRRMGWSGEPTTSELKNPERNISMGAAYLNILETGPLAGIEDPKVLQYALVVSYANGAGALLRTFSSDRKKAISKINDLDADEFLEHVARNHPAPQAPRYIYKLEQALDAMLEHHH 208
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208


Chain B from PDB  Type:PROTEIN  Length:188
 aligned with EMTA_ECOLI | P0C960 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:188
                                                                                                                                                                                                                 203    
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199   |    
           EMTA_ECOLI    20 HDYTNPPWNAKVPVQRAMQWMPISQKAGAAWGVDPQLITAIIAIESGGNPNAVSKSNAIGLMQLKASTSGRDVYRRMGWSGEPTTSELKNPERNISMGAAYLNILETGPLAGIEDPKVLQYALVVSYANGAGALLRTFSSDRKKAISKINDLDADEFLEHVARNHPAPQAPRYIYKLEQALDAM----   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------SLT-2y8pB01 B:41-169                                                                                                             -------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------SLT-2y8pB02 B:41-169                                                                                                             -------------------------------------- Pfam domains (2)
         Sec.struct. author .........hhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhh....................hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------TRANSGLYCOSYLASE  PDB: B:60-8----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y8p B  20 HDYTNPPWNAKVPVQRAMQWMPISQKAGAAWGVDPQLITAIIAIESGGNPNAVSKSNAIGLMQLKASTSGRDVYRRMGWSGEPTTSELKNPERNISMGAAYLNILETGPLAGIEDPKVLQYALVVSYANGAGALLRTFSSDRKKAISKINDLDADEFLEHVARNHPAPQAPRYIYKLEQALDAMLEHH 207
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199
   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  (0, 0)

(no "SCOP Domain" information available for 2Y8P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y8P)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Lysozyme (266)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (EMTA_ECOLI | P0C960)
molecular function
    GO:0016837    carbon-oxygen lyase activity, acting on polysaccharides    Catalysis of the cleavage of a carbon-oxygen bond by the elimination of an alcohol from a polysaccharide.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0008932    lytic endotransglycosylase activity    Catalysis of the specific cleavage of the beta-(1->4) glycosidic linkage between N-acetylmuramyl and N-acetylglucosaminyl residues in peptidoglycan, with the concomitant formation of 1,6-anhydro-N-acetylmuramyl residues. Acts on linkages within peptidoglycan chains (i.e. not at the ends) to produce shorter strands with 1,6-anhydromuramic acid ends.
    GO:0008933    lytic transglycosylase activity    Catalysis of the specific cleavage of the beta-(1->4) glycosidic linkage between N-acetylmuramyl and N-acetylglucosaminyl residues in peptidoglycan, with the concomitant formation of 1,6-anhydro-N-acetylmuramyl residues.
biological process
    GO:0016998    cell wall macromolecule catabolic process    The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
    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:0000270    peptidoglycan metabolic process    The chemical reactions and pathways involving peptidoglycans, any of a class of glycoconjugates found only in bacterial cell walls and consisting of strands of glycosaminoglycan cross-linked by oligopeptides to form a huge and rigid network.
    GO:0009254    peptidoglycan turnover    The continual breakdown and regeneration of peptidoglycan required to maintain the cell wall.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2y8p)
 
  Sites
(no "Sites" information available for 2y8p)
 
  Cis Peptide Bonds
    Asn A:24 - Pro A:25   [ RasMol ]  
    Asn B:24 - Pro B:25   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2y8p
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  EMTA_ECOLI | P0C960
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.2.2.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  EMTA_ECOLI | P0C960
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        EMTA_ECOLI | P0C960: 3t36 4hjv 4hjy 4hjz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Y8P)