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Asym./Biol. Unit (Jmol Viewer)

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Title :   ACCELERATED X-RAY STRUCTURE ELUCIDATION OF A 36 KDA MURAMIDASE/TRANSGLYCOSYLASE USING WARP

Authors :   E. J. Van Asselt, B. W. Dijkstra

Date :   26 Sep 97 (Deposition) - 11 Nov 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A

Keywords :   Glycosyltransferase, Muramidase, Transglycosylase, Peptidoglycan Maturation, Lysozyme, Periplasmic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. J. Van Asselt, A. Perrakis, K. H. Kalk, V. S. Lamzin, B. W. Dijkstra
Accelerated X-Ray Structure Elucidation Of A 36 Kda Muramidase/Transglycosylase Using Warp.
Acta Crystallogr. , Sect. D V. 54 58 1998
PubMed-ID: 9761817
(for further references see the PDB file header)

Molecule 1 - 36 KDA SOLUBLE LYTIC TRANSGLYCOSYLASE
	Cellular Location	:	PERIPLASM
	Cell Line	:	BL21
	Chains	:	A
	EC Number	:	3.2.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Plasmid	:	PAD115
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET21D+
	Fragment	:	SOLUBLE ACTIVE DOMAIN OF MLTB
	Gene	:	MLTB
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	122-1
	Synonym	:	35 KD SOLUBLE LYTIC TRANSGLYCOSYLASE, SLT35

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	BCN	1	Ligand/Ion	BICINE
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:237 , SER A:239 , ASP A:241 , HIS A:243 , ASP A:251	BINDING SITE FOR RESIDUE NA A 400
2	AC2	SOFTWARE	GLN A:225 , PHE A:226 , MET A:227 , SER A:230 , TYR A:259 , TYR A:338 , HOH A:616 , HOH A:651	BINDING SITE FOR RESIDUE BCN A 401
3	AC3	SOFTWARE	ARG A:188 , TYR A:191 , PHE A:192 , HOH A:708	BINDING SITE FOR RESIDUE EDO A 402

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:109	-	Pro A:110

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

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

(no "Exon" information available for 1LTM)

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:309
 aligned with MLTB_ECOLI | P41052 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:320
                                    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
           MLTB_ECOLI    42 EPQHNVMQMGGDFANNPNAQQFIDKMVNKHGFDRQQLQEILSQAKRLDSVLRLMDNQAPTTSVKPPSGPNGAWLRYRKKFITPDNVQNGVVFWNQYEDALNRAWQVYGVPPEIIVGIIGVETRWGRVMGKTRILDALATLSFNYPRRAEYFSGELETFLLMARDEQDDPLNLKGSFAGAMGYGQFMPSSYKQYAVDFSGDGHINLWDPVDAIGSVANYFKAHGWVKGDQVAVMANGQAPGLPNGFKTKYSISQLAAAGLTPQQPLGNHQQASLLRLDVGTGYQYWYGLPNFYTITRYNHSTHYAMAVWQLGQAVALARVQ 361
               SCOP domains d1ltma_ A: 36 kDa soluble lytic transglycosylase, SLT35                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------1ltmA02 A:109-167,A:248-361                                --------------------------------------------------------------------------------1ltmA02 A:109-167,A:248-361  [code=1.10.530.10, no name defined]                                                   CATH domains
               Pfam domains -------------SLT_2-1ltmA01 A:55-353                                                                                                                                                                                                                                                                                     -------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhh..-----------....hhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhh..........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......................hhhhhhh..............hhhhhhhhhhhhhh.........eee.................hhhhhh...............eeeeee....eeeeee.hhhhhhhh....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ltm A  42 EPQHNVMQMGGDFANNPNAQQFIDKMVNKHGFDRQQLQEILSQAKRLDSVLRLMDN-----------GPNGAWLRYRKKFITPDNVQNGVVFWNQYEDALNRAWQVYGVPPEIIVGIIGVETRWGRVMGKTRILDALATLSFNYPRRAEYFSGELETFLLMARDEQDDPLNLKGSFAGAMGYGQFMPSSYKQYAVDFSGDGHINLWDPVDAIGSVANYFKAHGWVKGDQVAVMANGQAPGLPNGFKTKYSISQLAAAGLTPQQPLGNHQQASLLRLDVGTGYQYWYGLPNFYTITRYNHSTHYAMAVWQLGQAVALARVQ 361
                                    51        61        71        81        91     |   -       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
                                                                                  97         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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Lysozyme-like (1361)

Superfamily: Lysozyme-like (1361)

Family: Bacterial muramidase, catalytic domain (11)

Protein domain: 36 kDa soluble lytic transglycosylase, SLT35 (8)

Escherichia coli [TaxId: 562] (8)

d1ltma_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Lysozyme (1131)

Homologous Superfamily: [code=1.10.530.10, no name defined] (605)

Escherichia coli. Organism_taxid: 562. Strain: 122-1. Cell_line: bl21. (1)

1ltmA02

A:109-167,A:248-361

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Lysozyme (266)

Family: SLT_2 (5)

Escherichia coli (strain K12) (5)

SLT_2-1ltmA01

A:55-353

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:109 - Pro A:110	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (3, 3)

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SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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