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(-) Description

Title :  2.1 A RESOLUTION STRUCTURE OF ESCHERICHIA COLI LYTIC TRANSGLYCOYSLASE SLT35 IN COMPLEX WITH CALCIUM
 
Authors :  E. J. Van Asselt, A. J. Dijkstra
Date :  10 Jul 99  (Deposition) - 24 Jan 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Helical Protein With An Five-Stranded Antiparallel Beta-Sheet, Glycosyl Transferase, Ef-Hand, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Van Asselt, B. W. Dijkstra
Binding Of Calcium In The Ef-Hand Of Escherichia Coli Lytic Transglycosylase Slt35 Is Important For Stability.
Febs Lett. V. 458 429 1999
PubMed-ID: 10570954  |  Reference-DOI: 10.1016/S0014-5793(99)01198-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LYTIC MUREIN TRANSGLYCOSYLASE B
    Cellular Location: PERIPLASM
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cellular Location: PERIPLASM
    Expression System Taxid: 562
    Fragment: SLT35
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: MUREIN HYDROLASE B, 35 KD SOLUBLE LYTIC TRANSGLYCOSYLASE, SLT35

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:237 , SER A:239 , ASP A:241 , HIS A:243 , ASP A:251 , HOH A:574BINDING SITE FOR RESIDUE CA A 400
2AC2SOFTWAREARG A:188BINDING SITE FOR RESIDUE EDO A 402
3AC3SOFTWAREGLN A:225 , PHE A:226 , MET A:227 , SER A:230 , TYR A:259 , TYR A:338BINDING SITE FOR RESIDUE GOL A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:109 -Pro A:110

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QDT)

(-) 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:312
 aligned with MLTB_ECOLI | P41052 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:322
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359  
           MLTB_ECOLI    40 LLEPQHNVMQMGGDFANNPNAQQFIDKMVNKHGFDRQQLQEILSQAKRLDSVLRLMDNQAPTTSVKPPSGPNGAWLRYRKKFITPDNVQNGVVFWNQYEDALNRAWQVYGVPPEIIVGIIGVETRWGRVMGKTRILDALATLSFNYPRRAEYFSGELETFLLMARDEQDDPLNLKGSFAGAMGYGQFMPSSYKQYAVDFSGDGHINLWDPVDAIGSVANYFKAHGWVKGDQVAVMANGQAPGLPNGFKTKYSISQLAAAGLTPQQPLGNHQQASLLRLDVGTGYQYWYGLPNFYTITRYNHSTHYAMAVWQLGQAVALARVQ 361
               SCOP domains d1qdta_ A: 36 kDa soluble lytic transglycosylase, SLT35                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------1qdtA02 A:109-167,A:248-361                                --------------------------------------------------------------------------------1qdtA02 A:109-167,A:248-361  [code=1.10.530.10, no name defined]                                                   CATH domains
               Pfam domains ---------------SLT_2-1qdtA01 A:55-353                                                                                                                                                                                                                                                                                     -------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhh.----------...hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee...........hhhhhhhhh............hhhhhhhhhhhhhhhh........eeeee........eeeeeeehhhhhhh..ee........eeeeeeee....eeeeeehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qdt A  40 MVEPQHNVMQMGGDFANNPNAQQFIDKMVNKHGFDRQQLQEILSQAKRLDSVLRLMDNQ----------GPNGAWLRYRKKFITPDNVQNGVVFWNQYEDALNRAWQVYGVPPEIIVGIIGVETRWGRVMGKTRILDALATLSFNYPRRAEYFSGELETFLLMARDEQDDPLNLKGSFAGAMGYGQFMPSSYKQYAVDFSGDGHINLWDPVDAIGSVANYFKAHGWVKGDQVAVMANGQAPGLPNGFKTKYSISQLAAAGLTPQQPLGNHQQASLLRLDVGTGYQYWYGLPNFYTITRYNHSTHYAMAVWQLGQAVALARVQ 361
                                    49        59        69        79        89        |-       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359  
                                                                                     98        109
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Lysozyme (266)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MLTB_ECOLI | P41052)
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: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: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.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MLTB_ECOLI | P41052: 1d0k 1d0l 1d0m 1ltm 1qdr 1qus 1qut

(-) Related Entries Specified in the PDB File

1qdr SLT35 IN COMPLEX WITH SODIUM
1qus HIGH RESOLUTION STRUCTURE OF SLT35
1qut SLT35 IN COMPLEX WITH N-ACETYL-D-GLUCOSAMINE