2Y68 - JenaLib

Title :   STRUCTURE-BASED DESIGN OF A NEW SERIES OF D-GLUTAMIC ACID-BASED INHIBITORS OF BACTERIAL MURD LIGASE

Authors :   T. Tomasic, N. Zidar, R. Sink, A. Kovac, D. Patin, D. Blanot, C. Contrera A. Dessen, M. Muller-Premru, A. Zega, S. Gobec, L. Peterlin-Masic, D.

Date :   20 Jan 11 (Deposition) - 08 Jun 11 (Release) - 31 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.49

Chains :   Asym./Biol. Unit : A

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

Reference :   T. Tomasic, N. Zidar, R. Sink, A. Kovac, D. Blanot, C. Contreras-Martel, A. Dessen, M. Muller-Premru, A. Zega, S. Gobec, D. Kikelj, L. Peterlin Masic
Structure-Based Design Of A New Series Of D- Glutamic Acid-Based Inhibitors Of Bacterial Udp-N- Acetylmuramoyl-L-Alanine:D-Glutamate Ligase (Murd).
J. Med. Chem. V. 54 4600 2011
PubMed-ID: 21591605 | Reference-DOI: 10.1021/JM2002525

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 15)

Sites (13, 13)

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ILE A:11 , ASP A:35 , THR A:36 , ARG A:37 , SER A:71 , ASN A:138 , PHE A:161 , HIS A:183 , LYS A:348 , ALA A:414 , SER A:415 , ASN A:421 , PHE A:422 , SO4 A:1442 , HOH A:2166 , HOH A:2193 , HOH A:2234 , HOH A:2439 , HOH A:2440 , HOH A:2441 , HOH A:2443 , HOH A:2447	BINDING SITE FOR RESIDUE T04 A 500
02	AC2	SOFTWARE	LEU A:163 , THR A:166 , SER A:167 , SER A:168 , LEU A:169 , ARG A:200 , GLU A:203	BINDING SITE FOR RESIDUE DMS A 601
03	AC3	SOFTWARE	ASN A:7 , ARG A:32 , ALA A:64 , GLU A:308 , HIS A:309 , ASN A:310	BINDING SITE FOR RESIDUE DMS A 604
04	AC4	SOFTWARE	GLN A:418 , PHE A:419	BINDING SITE FOR RESIDUE AZI A 700
05	AC5	SOFTWARE	ALA A:329 , ASN A:331 , GLY A:332 , LEU A:333	BINDING SITE FOR RESIDUE AZI A 701
06	AC6	SOFTWARE	LEU A:339 , ASN A:363 , VAL A:364	BINDING SITE FOR RESIDUE AZI A 703
07	AC7	SOFTWARE	ALA A:104 , PRO A:105 , HOH A:2138 , HOH A:2444	BINDING SITE FOR RESIDUE AZI A 704
08	AC8	SOFTWARE	ASN A:113 , GLY A:114 , LYS A:115 , SER A:116 , THR A:117 , ARG A:302 , HOH A:2445 , HOH A:2446	BINDING SITE FOR RESIDUE SO4 A1440
09	AC9	SOFTWARE	HIS A:309 , ASN A:310 , SER A:438 , HIS A:439	BINDING SITE FOR RESIDUE SO4 A1441
10	BC1	SOFTWARE	GLY A:14 , LEU A:15 , THR A:16 , T04 A:500 , HOH A:2447 , HOH A:2448 , HOH A:2449	BINDING SITE FOR RESIDUE SO4 A1442
11	BC2	SOFTWARE	ARG A:37 , MET A:38 , GLN A:170	BINDING SITE FOR RESIDUE SO4 A1443
12	BC3	SOFTWARE	ARG A:395	BINDING SITE FOR RESIDUE CL A1444
13	BC4	SOFTWARE	SER A:56 , LEU A:57 , HOH A:2103	BINDING SITE FOR RESIDUE CL A1445

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

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------Mur_ligase_M-2y68A02 A:109-279                                                                                                                                             -------------------Mur_ligase_C-2y68A01 A:299-378                                                  ------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.hhhhhhhhhhhhhhh....eeee......hhhhh.....eee...hhhhhhhh.eeee.......hhhhhhhhhh..eeehhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh...eeeee....hhhhhh.....eeeee.hhhhhhh.......eeee......hhhhh.hhhhhhhhhhhhhhh....eeee..hhhhh...----..eee......eeeeee..eeeeee..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
                 2y68 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

Legend:		→ Mismatch	(orange background)
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		→ 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 (0, 0)

CATH Domains (0, 0)

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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	2y68
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1e0d	UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
1eeh	UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
1uag	UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
2jff	CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING SULFONAMIDE INHIBITOR
2jfg	CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH UMA AND ADP
2jfh	CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH L-GLU CONTAINING SULFONAMIDE INHIBITOR
2uag	UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
2uuo	CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING SULFONAMIDE INHIBITOR
2uup	CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING SULFONAMIDE INHIBITOR
2vtd	CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING SULFONAMIDE INHIBITOR
2vte	CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING SULFONAMIDE INHIBITOR
2wjp	CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING RHODANINE INHIBITOR
2x5o	DISCOVERY OF NOVEL 5-BENZYLIDENERHODANINE- AND 5-BENZYLIDENE-THIAZOLIDINE-2,4-DIONE INHIBITORS OF MURD LIGASE
2y1o	DUAL-TARGET INHIBITOR OF MURD AND MURE LIGASES: DESIGN, SYNTHESIS AND BINDING MODE STUDIES
2y66	NEW 5-BENZYLIDENETHIAZOLIDINE-4-ONE INHIBITORS OF BACTERIAL MURD LIGASE: DESIGN, SYNTHESIS, CRYSTAL STRUCTURES, AND BIOLOGICAL EVALUATION
2y67	NEW 5-BENZYLIDENETHIAZOLIDINE-4-ONE INHIBITORS OF BACTERIAL MURD LIGASE: DESIGN, SYNTHESIS, CRYSTAL STRUCTURES, AND BIOLOGICAL EVALUATION
3uag	UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
4uag	UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE

Description