3TUR - JenaLib

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Title :   CRYSTAL STRUCTURE OF M. TUBERCULOSIS LD-TRANSPEPTIDASE TYPE 2 COMPLEXED WITH A PEPTIDOGLYCAN FRAGMENT

Authors :   M. A. Bianchet, S. B. Erdemli, R. Gupta, G. Lamichhane, L. M. Amzel

Date :   17 Sep 11 (Deposition) - 05 Dec 12 (Release) - 26 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.72

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Protein-Peptidoglycan Complex, Peptidoglycan Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. B. Erdemli, R. Gupta, W. R. Bishai, G. Lamichhane, L. M. Amzel, M. A. Bianchet
Targeting The Cell Wall Of Mycobacterium Tuberculosis: Structure And Mechanism Of L, D-Transpeptidase 2.
Structure V. 20 2103 2012
PubMed-ID: 23103390 | Reference-DOI: 10.1016/J.STR.2012.09.016

Molecule 1 - MYCOBACTERIA TUBERCULOSIS LD-TRANSPEPTIDASE TYPE 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	LPPS, MT2594, RV2518C
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 11)

No.	Name	Count	Type	Full Name
1	0JC	8	Ligand/Ion	DI-MU-IODOBIS(ETHYLENEDIAMINE)DIPLATINUM(II)
2	6CL	1	Ligand/Ion	6-CARBOXYLYSINE
3	DGL	1	Ligand/Ion	D-GLUTAMIC ACID
4	PT	1	Ligand/Ion	PLATINUM (II) ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	0JC	4	Ligand/Ion	DI-MU-IODOBIS(ETHYLENEDIAMINE)DIPLATINUM(II)
2	6CL	1	Ligand/Ion	6-CARBOXYLYSINE
3	DGL	1	Ligand/Ion	D-GLUTAMIC ACID
4	PT	-1	Ligand/Ion	PLATINUM (II) ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	0JC	4	Ligand/Ion	DI-MU-IODOBIS(ETHYLENEDIAMINE)DIPLATINUM(II)
2	6CL	-1	Ligand/Ion	6-CARBOXYLYSINE
3	DGL	-1	Ligand/Ion	D-GLUTAMIC ACID
4	PT	-1	Ligand/Ion	PLATINUM (II) ION

Biological Unit 3 (3, 10)

No.	Name	Count	Type	Full Name
1	0JC	8	Ligand/Ion	DI-MU-IODOBIS(ETHYLENEDIAMINE)DIPLATINUM(II)
2	6CL	1	Ligand/Ion	6-CARBOXYLYSINE
3	DGL	1	Ligand/Ion	D-GLUTAMIC ACID
4	PT	-1	Ligand/Ion	PLATINUM (II) ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:346 , HIS A:347	BINDING SITE FOR RESIDUE 0JC A 501
02	AC2	SOFTWARE	MET A:157 , ALA A:171 , ARG A:173 , ARG A:209 , TYR A:330 , HOH A:737	BINDING SITE FOR RESIDUE 0JC A 502
03	AC3	SOFTWARE	HIS A:150 , GLU A:235 , MET A:237	BINDING SITE FOR RESIDUE 0JC A 503
04	AC4	SOFTWARE	GLU A:213 , HIS A:214 , PHE A:215 , ILE A:291	BINDING SITE FOR RESIDUE 0JC A 504
05	AC5	SOFTWARE	TYR A:318 , THR A:320 , TRP A:340 , HIS A:352 , 6CL A:506 , HOH A:645 , HOH A:738 , THR B:320 , TRP B:340 , HIS B:352 , HOH B:605	BINDING SITE FOR RESIDUE DGL A 505
06	AC6	SOFTWARE	TYR A:318 , SER A:331 , GLY A:332 , HIS A:336 , TRP A:340 , SER A:351 , HIS A:352 , GLY A:353 , CYS A:354 , ASN A:356 , DGL A:505 , HOH A:614 , HOH A:659 , HOH A:680 , HOH A:828 , TYR B:318 , SER B:331 , GLY B:332 , HIS B:336 , TRP B:340 , SER B:351 , HIS B:352 , GLY B:353 , CYS B:354 , ASN B:356 , HOH B:836	BINDING SITE FOR RESIDUE 6CL A 506
07	AC7	SOFTWARE	MET B:237	BINDING SITE FOR RESIDUE PT B 501
08	AC8	SOFTWARE	GLY B:346 , HIS B:347 , HOH B:718	BINDING SITE FOR RESIDUE 0JC B 502
09	AC9	SOFTWARE	GLU B:213 , HIS B:214 , PHE B:215 , HOH B:624	BINDING SITE FOR RESIDUE 0JC B 503
10	BC1	SOFTWARE	MET B:157 , ALA B:171 , ARG B:173 , ARG B:209 , TYR B:330 , HOH B:623 , HOH B:782 , HOH B:838 , HOH B:841	BINDING SITE FOR RESIDUE 0JC B 504
11	BC2	SOFTWARE	MET B:153 , GLU B:240	BINDING SITE FOR RESIDUE 0JC B 505

(no "SS Bond" information available for 3TUR)

Asymmetric Unit

No.	Residues
1	Met A:157	-	Pro A:158
2	Asn A:193	-	Pro A:194
3	Met B:157	-	Pro B:158
4	Asn B:193	-	Pro B:194

(no "SAP(SNP)/Variant" information available for 3TUR)

(no "PROSITE Motif" information available for 3TUR)

(no "Exon" information available for 3TUR)

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:258
 aligned with LDT2_MYCTO | O53223 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:258
                                   159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399        
           LDT2_MYCTO   150 HLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAK 407
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.eeee.....ee.....eeeee.....hhhhhhhheeeeee....eeeeeee..eeeeee........eeeeeee..........ee..eeeeeeee...eeeeee....eeeeee..eeeeeee............eeee...eeeeeeee.hhhh.........eeeeeeeee......eeee.hhhh............eeehhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tur A 150 HLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAK 407
                                   159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399

Chain B from PDB  Type:PROTEIN  Length:269
 aligned with LDT2_MYCTO | O53223 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:286
                                   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       381       391       401      
           LDT2_MYCTO   122 RRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAK 407
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.....-----------------.ee.eeee.....ee.....eeeee.....hhhhhhhheeeeee....eeeee....eeeeee........eeeeee.....eee..eee...eeeeeee...eeeeee....eeeeee..eeeeeee............eeee...eeeeeeee.hhhh.........eeeeeeeee......eeee.hhhh............eeehhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tur B 122 RRYTLNATALG-----------------HLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAK 407
                                   131|        -       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401      
                                    132               150

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 '\|'

(no "SCOP Domain" information available for 3TUR)

(no "CATH Domain" information available for 3TUR)

(no "Pfam Domain" information available for 3TUR)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LDT2_MYCTO | O53223)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0071972	peptidoglycan L,D-transpeptidase activity	Catalysis of the reaction: 2 a peptidoglycan dimer (tetrapeptide) + 3 H2O = a peptidoglycan tetramer with L,D cross-links (L-Lys-D-Asn-L-Lys) + di-trans,poly-cis-undecaprenyl diphosphate + 4 D-alanine.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
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:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	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: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:0009273	peptidoglycan-based cell wall biogenesis	The chemical reactions and pathways resulting in the formation of the peptidoglycan-based cell wall. An example of this process is found in Escherichia coli.
	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:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	Cis Peptide Bonds
		Asn A:193 - Pro A:194	[ RasMol ]
		Asn B:193 - Pro B:194	[ RasMol ]
		Met A:157 - Pro A:158	[ RasMol ]
		Met B:157 - Pro B:158	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (14, 14)

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