4BUB - JenaLib

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Title :   CRYSTAL STRUCTURE OF MURE LIGASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH ADP

Authors :   S. Favini-Stabile, C. Contreras-Martel, N. Thielens, A. Dessen

Date :   20 Jun 13 (Deposition) - 17 Jul 13 (Release) - 18 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Ligase, Peptidoglycan Synthesis, Mure, Adp-Forming Enzyme, Cell Wall, Cell Shape, Cell Cycle, Nucleotide-Binding, Atp- Binding, Cell Division (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Favini-Stabile, C. Contreras-Martel, N. Thielens, A. Dessen
Mreb And Murg As Scaffolds For The Cytoplasmic Steps Of Peptidoglycan Biosynthesis
Environ. Microbiol. V. 15 3218 2013
PubMed-ID: 23826965 | Reference-DOI: 10.1111/1462-2920.12171

Molecule 1 - UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--LD-LYSINE LIGASE
	Chains	:	A, B
	EC Number	:	6.3.2.37, 6.3.2.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET30B
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Strain	:	DSM 3109
	Synonym	:	MURD LIGASE, D-GLUTAMIC ACID-ADDING ENZYME, UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE SYNTHETASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 22)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 10)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:111 , ASN A:112 , GLY A:113 , LYS A:114 , THR A:115 , THR A:116 , ASN A:200 , ASN A:296 , ARG A:327 , ALA A:351 , LYS A:354 , MG A:1487	BINDING SITE FOR RESIDUE ADP A1486
2	AC2	SOFTWARE	THR A:137 , GLU A:177 , ADP A:1486	BINDING SITE FOR RESIDUE MG A1487
3	AC3	SOFTWARE	THR B:111 , ASN B:112 , GLY B:113 , LYS B:114 , THR B:115 , GLU B:177 , ASN B:200 , PHE B:292 , ASN B:296 , ARG B:327 , MG B:1487	BINDING SITE FOR RESIDUE ADP B1486
4	AC4	SOFTWARE	THR B:115 , THR B:137 , ADP B:1486	BINDING SITE FOR RESIDUE MG B1487

(no "SS Bond" information available for 4BUB)

(no "Cis Peptide Bond" information available for 4BUB)

(no "SAP(SNP)/Variant" information available for 4BUB)

(no "PROSITE Motif" information available for 4BUB)

(no "Exon" information available for 4BUB)

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:478
 aligned with MURE_THEMA | Q9WY79 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:485
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480     
           MURE_THEMA     1 MNISTIVSNLKDLILEVRAPYDLEITGVSNHSSKVKKGDLFICRRGEKFDSHEIIPEVMEKGAVAVVVEREIDLDFPYIQVFDSRYFEAKVASLFFEDPWKDVLTFGVTGTNGKTTTTMMIYHMLTSLGERGSVLTTAVKRILGNSYYDDITTPDAITILSAMKENREGGGKFFALEVSSHALVQQRVEGVRFDVGIFTNISRDHLDFHGTFENYLKAKLHLFDLLKDDGVAVLNESLADAFNRKSRKITFGTSKNADYRLGNIEVSWEGTQFVLETPDGLLKVFTRAIGDFNAYNAAAAIAALHQLGYDPKDLASSLETFTGVEGRFEVVRGAKKIGLNVVVDFAHSPDALEKLLKNVRKISQGRVIVVFGAGGNSDRGKRPMMSEVASKLADVVILTTDDPRGEDPEQIMEDLIKGIDKRKPYLVLFDRREAIETALTIANRGDSVVIAGRGHERYQIIDEEKKVPFQDREVVEEIIRDKLKG 485
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...eeeee........eee.........eeeee..-------hhhhhhhhh...eeee.........eeee.hhhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhh.....eee....ee.............hhhhhhhhhhhhhhh...eeeee...hhhhhh......eeeeee............hhhhhhhhhhhhhh.eeeeeeeeee.hhh.......eeeeee......eee..........eeeee.....eeee......hhhhhhhhhhhhhhh...hhhhhhh............ee.hhhh....eeee....hhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhh.eeee.........hhhhhhhhhh.......eee..hhhhhhhhhhhhh....eeee.......eeeee..eeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bub A   1 mNISTIVSNLKDLILEVRAPYDLEITGVSNHSSKVKKGDLFICRR-------EIIPEVmEKGAVAVVVEREIDLDFPYIQVFDSRYFEAKVASLFFEDPWKDVLTFGVTGTNGKTTTTmmIYHmLTSLGERGSVLTTAVKRILGNSYYDDITTPDAITILSAmKENREGGGKFFALEVSSHALVQQRVEGVRFDVGIFTNISRDHLDFHGTFENYLKAKLHLFDLLKDDGVAVLNESLADAFNRKSRKITFGTSKNADYRLGNIEVSWEGTQFVLETPDGLLKVFTRAIGDFNAYNAAAAIAALHQLGYDPKDLASSLETFTGVEGRFEVVRGAKKIGLNVVVDFAHSPDALEKLLKNVRKISQGRVIVVFGAGGNSDRGKRPmmSEVASKLADVVILTTDDPRGEDPEQImEDLIKGIDKRKPYLVLFDRREAIETALTIANRGDSVVIAGRGHERYQIIDEEKKVPFQDREVVEEIIRDKLKG 485
                            |       10        20        30        40    |    -  |     60        70        80        90       100       110       120   |   130       140       150       160  |    170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380   ||  390       400       410 |     420       430       440       450       460       470       480     
                            |                                          45      53     |                                                         119-MSE|                                    163-MSE                                                                                                                                                                                                                      384-MSE                     412-MSE                                                                     
                            1-MSE                                                    59-MSE                                                      120-MSE                                                                                                                                                                                                                                                                  385-MSE                                                                                                
                                                                                                                                                     124-MSE

Chain B from PDB  Type:PROTEIN  Length:483
 aligned with MURE_THEMA | Q9WY79 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:485
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480     
           MURE_THEMA     1 MNISTIVSNLKDLILEVRAPYDLEITGVSNHSSKVKKGDLFICRRGEKFDSHEIIPEVMEKGAVAVVVEREIDLDFPYIQVFDSRYFEAKVASLFFEDPWKDVLTFGVTGTNGKTTTTMMIYHMLTSLGERGSVLTTAVKRILGNSYYDDITTPDAITILSAMKENREGGGKFFALEVSSHALVQQRVEGVRFDVGIFTNISRDHLDFHGTFENYLKAKLHLFDLLKDDGVAVLNESLADAFNRKSRKITFGTSKNADYRLGNIEVSWEGTQFVLETPDGLLKVFTRAIGDFNAYNAAAAIAALHQLGYDPKDLASSLETFTGVEGRFEVVRGAKKIGLNVVVDFAHSPDALEKLLKNVRKISQGRVIVVFGAGGNSDRGKRPMMSEVASKLADVVILTTDDPRGEDPEQIMEDLIKGIDKRKPYLVLFDRREAIETALTIANRGDSVVIAGRGHERYQIIDEEKKVPFQDREVVEEIIRDKLKG 485
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...eee..........eee.........eeee.....--hhhhhhhhhhhh....eee.........eeee.hhhhhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhh.....ee....ee.............hhhhhhhhhhhhhhhh..eeeee.hhhhhhh.......eeeeee............hhhhhhhhhhhhhh.eeeeeeeeee.hhh........eeeee......eeeeeeeee..eeeeeee.....eeeee.....hhhhhhhhhhhhhhh...hhhhhhh............eeehhhh....eeee....hhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhh.eeee........hhhhhhhhhhh.......eee..hhhhhhhhhhhhh....eeee.......eeeee..eeee.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bub B   1 mNISTIVSNLKDLILEVRAPYDLEITGVSNHSSKVKKGDLFICRRGE--DSHEIIPEVmEKGAVAVVVEREIDLDFPYIQVFDSRYFEAKVASLFFEDPWKDVLTFGVTGTNGKTTTTmmIYHmLTSLGERGSVLTTAVKRILGNSYYDDITTPDAITILSAmKENREGGGKFFALEVSSHALVQQRVEGVRFDVGIFTNISRDHLDFHGTFENYLKAKLHLFDLLKDDGVAVLNESLADAFNRKSRKITFGTSKNADYRLGNIEVSWEGTQFVLETPDGLLKVFTRAIGDFNAYNAAAAIAALHQLGYDPKDLASSLETFTGVEGRFEVVRGAKKIGLNVVVDFAHSPDALEKLLKNVRKISQGRVIVVFGAGGNSDRGKRPmmSEVASKLADVVILTTDDPRGEDPEQImEDLIKGIDKRKPYLVLFDRREAIETALTIANRGDSVVIAGRGHERYQIIDEEKKVPFQDREVVEEIIRDKLKG 485
                            |       10        20        30        40      | 50        60        70        80        90       100       110       120   |   130       140       150       160  |    170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380   ||  390       400       410 |     420       430       440       450       460       470       480     
                            1-MSE                                        47 50       59-MSE                                                     119-MSE|                                    163-MSE                                                                                                                                                                                                                      384-MSE                     412-MSE                                                                     
                                                                                                                                                 120-MSE                                                                                                                                                                                                                                                                  385-MSE                                                                                                
                                                                                                                                                     124-MSE

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 4BUB)

(no "CATH Domain" information available for 4BUB)

(no "Pfam Domain" information available for 4BUB)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MURE_THEMA | Q9WY79)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0047482	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase activity	Catalysis of the reaction: L-lysine + ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate = ADP + 2 H(+) + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine.
	GO:0016881	acid-amino acid ligase activity	Catalysis of the ligation of an acid to an amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0004326	tetrahydrofolylpolyglutamate synthase activity	Catalysis of the reaction: ATP + tetrahydrofolyl-(Glu)(n) + L-glutamate = ADP + phosphate + tetrahydrofolyl-(Glu)(n+1).
biological process
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	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:0009396	folic acid-containing compound biosynthetic process	The chemical reactions and pathways resulting in the formation of folic acid and its derivatives.
	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:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	GO:0046901	tetrahydrofolylpolyglutamate biosynthetic process	The chemical reactions and pathways resulting in the formation of tetrahydrofolylpolyglutamate, a folate derivative comprising tetrahydrofolate attached to a chain of glutamate residues.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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4buc	CRYSTAL STRUCTURE OF MURD LIGASE FROM THERMOTOGA MARITIMA IN APO FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 22)

Sites (4, 4)

SS Bonds (0, 0)

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