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Title :   CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING RHODANINE INHIBITOR

Authors :   T. Tomasic, N. Zidar, R. Sink, A. Kovac, V. Rupnik, S. Turk, C. Contreras A. Dessen, D. Blanot, M. Muller-Premru, S. Gobec, A. Zega, L. Peterlin D. Kikelj

Date :   28 May 09 (Deposition) - 25 Aug 10 (Release) - 26 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A

Keywords :   Peptidoglycan Synthesis, Cell Wall Biogenesis/Degradation, Cell Cycle, Cell Division, Ligase, Cell Shape Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Zidar, T. Tomasic, R. Sink, V. Rupnik, A. Kovac, S. Turk, D. Patin, D. Blanot, C. Contreras Martel, A. Dessen, M. Muller Premru, A. Zega S. Gobec, L. Peterlin Masic, D. Kikelj
Discovery Of Novel 5-Benzylidenerhodanine And 5- Benzylidenethiazolidine-2, 4-Dione Inhibitors Of Murd Ligase
J. Med. Chem. V. 53 6584 2010
PubMed-ID: 20804196 | Reference-DOI: 10.1021/JM100285G

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 19)

Sites (17, 17)

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ILE A:11 , ASP A:35 , THR A:36 , ARG A:37 , SER A:71 , PRO A:72 , PHE A:161 , HIS A:183 , LYS A:348 , ALA A:414 , SER A:415 , LEU A:416 , ASN A:421 , PHE A:422 , SO4 A:1451 , HOH A:2525 , HOH A:2526 , HOH A:2528 , HOH A:2529 , HOH A:2530	BINDING SITE FOR RESIDUE D17 A1441
02	AC2	SOFTWARE	GLY A:73 , ARG A:186 , LEU A:416 , HOH A:2265 , HOH A:2529 , HOH A:2531	BINDING SITE FOR RESIDUE DMS A1442
03	AC3	SOFTWARE	ASP A:417 , GLN A:418 , PHE A:419	BINDING SITE FOR RESIDUE AZI A1443
04	AC4	SOFTWARE	ALA A:329 , ASN A:331 , LEU A:333 , HOH A:2532	BINDING SITE FOR RESIDUE AZI A1444
05	AC5	SOFTWARE	PRO A:300 , ARG A:302 , PHE A:422 , GLU A:423	BINDING SITE FOR RESIDUE AZI A1445
06	AC6	SOFTWARE	LEU A:339 , ASN A:363	BINDING SITE FOR RESIDUE AZI A1446
07	AC7	SOFTWARE	ALA A:102 , ALA A:104 , PRO A:105 , HOH A:2164	BINDING SITE FOR RESIDUE AZI A1447
08	AC8	SOFTWARE	ASN A:113 , GLY A:114 , LYS A:115 , SER A:116 , THR A:117 , ARG A:302 , HOH A:2533 , HOH A:2534	BINDING SITE FOR RESIDUE SO4 A1448
09	AC9	SOFTWARE	THR A:166 , SER A:167 , SER A:168 , LEU A:169 , ARG A:200 , GLU A:203	BINDING SITE FOR RESIDUE SO4 A1449
10	BC1	SOFTWARE	HIS A:309 , ASN A:310 , SER A:438 , HIS A:439	BINDING SITE FOR RESIDUE SO4 A1450
11	BC2	SOFTWARE	GLY A:14 , LEU A:15 , THR A:16 , D17 A:1441 , HOH A:2024 , HOH A:2526 , HOH A:2535 , HOH A:2536	BINDING SITE FOR RESIDUE SO4 A1451
12	BC3	SOFTWARE	ARG A:37 , MET A:38 , GLN A:170 , HOH A:2537	BINDING SITE FOR RESIDUE SO4 A1452
13	BC4	SOFTWARE	HIS A:309 , ASN A:310 , HOH A:2055 , HOH A:2057	BINDING SITE FOR RESIDUE CL A1453
14	BC5	SOFTWARE	ARG A:395	BINDING SITE FOR RESIDUE CL A1454
15	BC6	SOFTWARE	TYR A:3 , GLN A:4 , ARG A:27	BINDING SITE FOR RESIDUE CL A1455
16	BC7	SOFTWARE	GLU A:96 , THR A:165 , SER A:167 , HOH A:2149	BINDING SITE FOR RESIDUE CL A1456
17	BC8	SOFTWARE	LEU A:57 , HOH A:2127	BINDING SITE FOR RESIDUE CL A1457

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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

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Chain A from PDB  Type:PROTEIN  Length:435
 aligned with MURD_ECOLI | P14900 from UniProtKB/Swiss-Prot  Length:438

    Alignment length:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              438  
                                    11        21        31        41        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       371       381       391       401       411       421       431      |  
           MURD_ECOLI     2 ADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAVERHTGSLNDEWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCREAQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDECELYVLELSSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAKLRIYENAKVCVVNADDALTMPIRGADERCVSFGVNMGDYHLNHQQGETWLRVKGEKVLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFEVVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSPLARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPRVQPGDMVLLSPACASLDQFKNFEQRGNEFARLAKELG--   -
               SCOP domains d2wjpa1 A:1-93 automated matches                                                             d2wjpa2 A:94-297 automated matches                                                                                                                                                                          d2wjpa3 A:298-439 automated matches                                                                                                            SCOP domains
               CATH domains 2wjpA01 A:1-92 NAD(P)-binding Rossmann-like Domain                                          2wjpA02 A:93-298  [code=3.40.1190.10, no name defined]                                                                                                                                                        2wjpA03 A:299-433  [code=3.90.190.20, no name defined]                                                                                 ------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------Mur_ligase_M-2wjpA02 A:109-279                                                                                                                                             -------------------Mur_ligase_C-2wjpA01 A:299-378                                                  ------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.hhhhhhhhhhhhhh.....eeee......hhhhh.....eee...hhhhhhh..eeee.......hhhhhhhhhh..eeehhhhhhhh.....eeeee...hhhhhhhhhhhhhhhh...eeeee....hhhhhh.....eeeee.hhhhhhh.......eeee......hhhhh.hhhhhhhhh..........eeee..hhhhh...----..eee......eeeee....eeeee..eeeee.hhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.......eeeeee..eeeee.....hhhhhhhhhh.......eeeeee.......hhhhhhhh....eeeeee..hhhhhhhhhhh.eee..hhhhhhhhhhhhh....eeee...........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wjp A   1 ADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAVERHTGSLNDEWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCREAQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDECELYVLELSSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAkLRIYENAKVCVVNADDALTMPIR----RCVSFGVNMGDYHLNHQQGETWLRVKGEKVLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFEVVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSPLARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPRVQPGDMVLLSPACASLDQFKNFEQRGNEFARLAKELGSH 439
                                    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         
                                                                                                                                                                                                                               198-KCX                221  226

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	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 (3, 3)

CATH Domains (3, 3)

Pfam Domains (2, 2)

Gene Ontology (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MURD_ECOLI | P14900)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008764	UDP-N-acetylmuramoylalanine-D-glutamate ligase activity	Catalysis of the reaction: D-glutamate + ATP + UDP-N-acetylmuramoyl-L-alanine = ADP + 2 H(+) + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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: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.
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: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.
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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