2I87 - JenaLib

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Title :   ALLOSTERIC INHIBITION OF STAPHYLOCOCCUS AUREUS D-ALANINE:D-ALANINE LIGASE REVEALED BY CRYSTALLOGRAPHIC STUDIES

Authors :   S. Liu, J. S. Chang, J. T. Herberg, M. Horng, P. K. Tomich, A. H. Lin, K. R. M

Date :   01 Sep 06 (Deposition) - 03 Oct 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   D-Alanine:D-Alanine Ligase, Apo, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Liu, J. S. Chang, J. T. Herberg, M. M. Horng, P. K. Tomich, A. H. Lin, K. R. Marotti
Allosteric Inhibition Of Staphylococcus Aureus D-Alanine:D-Alanine Ligase Revealed By Crystallographic Studies.
Proc. Natl. Acad. Sci. Usa V. 103 15178 2006
PubMed-ID: 17015835 | Reference-DOI: 10.1073/PNAS.0604905103

Molecule 1 - D-ALANINE-D-ALANINE LIGASE
	Chains	:	A, B
	EC Number	:	6.3.2.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE-60
	Expression System Strain	:	M15[PREP4]
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DDL
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
	Organism Taxid	:	93062
	Strain	:	COL
	Synonym	:	D-ALANYLALANINE SYNTHETASE, D-ALA-D-ALA LIGASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:291 , ASN A:308 , PRO A:311 , GLY A:312	BINDING SITE FOR RESIDUE SO4 A 401
2	AC2	SOFTWARE	ARG B:291 , ASN B:308 , PRO B:311 , GLY B:312	BINDING SITE FOR RESIDUE SO4 B 402

(no "SS Bond" information available for 2I87)

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:172	-	Pro A:173
2	Ile A:261	-	Pro A:262
3	Tyr B:172	-	Pro B:173
4	Ile B:261	-	Pro B:262

(no "SAP(SNP)/Variant" information available for 2I87)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DALA_DALA_LIGASE_1	PS00843	D-alanine--D-alanine ligase signature 1.	DDL_STAAC	96-107	2	A:96-107 B:96-107
2	DALA_DALA_LIGASE_2	PS00844	D-alanine--D-alanine ligase signature 2.	DDL_STAAC	284-312	2	A:284-312 B:284-312

(no "Exon" information available for 2I87)

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:345
 aligned with DDL_STAAC | Q5HEB7 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:356
                                                                                                                                                                                                                                                                                                                                                                                           356  
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352   |  
            DDL_STAAC     3 KENICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTDELHLENGEALEISQLLKESSSGQPYDAVFPLLHGPNGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVNDKLNYPVFVKPANLGSSVGISKCNNEAELKEGIKEAFQFDRKLVIEQGVNAREIEVAVLGNDYPEATWPGEVVKDVAFYDYKSKYKDGKVQLQIPADLDEDVQLTLRNMALEAFKATDCSGLVRADFFVTEDNQIYINETNAMPGFTAFSMYPKLWENMGLSYPELITKLIELAKERHQDKQKNKYKID--   -
               SCOP domains d2i87a1 A:3-128 automated matches                                                                                             d2i87a2 A:129-358 automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhhhhh.....eeeeeeee.....eeee........hhhhhhhhhheee..hhhhhh........eeeee........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh...eeeee.........eee.hhhhhhhhhhhhhh...eeeeee....eeeeeeeee....ee...eee......-----------..ee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------DALA_DALA_LI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           ---------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i87 A   3 KENICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTDELHLENGEALEISQLLKESSSGQPYDAVFPLLHGPNGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVNDKLNYPVFVKPANLGSSVGISKCNNEAELKEGIKEAFQFDRKLVIEQGVNAREIEVAVLGNDYPEATWPGEVVKDVAF-----------VQLQIPADLDEDVQLTLRNMALEAFKATDCSGLVRADFFVTEDNQIYINETNAMPGFTAFSMYPKLWENMGLSYPELITKLIELAKERHQDKQKNKYKIDRS 358
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242  |      -    |  262       272       282       292       302       312       322       332       342       352      
                                                                                                                                                                                                                                                                            245         257

Chain B from PDB  Type:PROTEIN  Length:344
 aligned with DDL_STAAC | Q5HEB7 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:358
                                                                                                                                                                                                                                                                                                                                                                                           356    
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352   |    
            DDL_STAAC     3 KENICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTDELHLENGEALEISQLLKESSSGQPYDAVFPLLHGPNGEDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVNDKLNYPVFVKPANLGSSVGISKCNNEAELKEGIKEAFQFDRKLVIEQGVNAREIEVAVLGNDYPEATWPGEVVKDVAFYDYKSKYKDGKVQLQIPADLDEDVQLTLRNMALEAFKATDCSGLVRADFFVTEDNQIYINETNAMPGFTAFSMYPKLWENMGLSYPELITKLIELAKERHQDKQKNKYKID----   -
               SCOP domains d2i87b1 B:3-128 automated matches                                                                                             d2i87b2 B:129-360 automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee.....eeee........hhhhhh.....-.hhhhhhhh........eeee.....--..hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh...eeeee.........eee.hhhhhhhhhhhhh....eeeeee....eeeeeeeee....ee...eee......-----------..ee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------DALA_DALA_LI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           ------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i87 B   3 KENICIVFGGKSAEHEVSILTAQNVLNAIDKDKYHVDIIYITNDGDWRKQNNITAEIKSTDELHLENGE-LEISQLLKESSSGQPYDAVFPLLHGP--EDGTIQGLFEVLDVPYVGNGVLSAASSMDKLVMKQLFEHRGLPQLPYISFLRSEYEKYEHNILKLVNDKLNYPVFVKPANLGSSVGISKCNNEAELKEGIKEAFQFDRKLVIEQGVNAREIEVAVLGNDYPEATWPGEVVKDVAF-----------VQLQIPADLDEDVQLTLRNMALEAFKATDCSGLVRADFFVTEDNQIYINETNAMPGFTAFSMYPKLWENMGLSYPELITKLIELAKERHQDKQKNKYKIDRSHH 360
                                    12        22        32        42        52        62        |-|       82        92     | 102       112       122       132       142       152       162       172       182       192       202       212       222       232       242  |      -    |  262       272       282       292       302       312       322       332       342       352        
                                                                                               71 |                       98  |                                                                                                                                             245         257                                                                                                       
                                                                                                 73                         101

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: ATP-grasp (191)

Superfamily: Glutathione synthetase ATP-binding domain-like (158)

Family: automated matches (42)

Protein domain: automated matches (42)

Staphylococcus aureus [TaxId: 93062] (2)

1a	d2i87a2	A:129-358
1b	d2i87b2	B:129-360

Class: Alpha and beta proteins (a/b) (23833)

Fold: PreATP-grasp domain (131)

Superfamily: PreATP-grasp domain (131)

Family: automated matches (45)

Protein domain: automated matches (45)

Staphylococcus aureus [TaxId: 93062] (2)

2a	d2i87a1	A:3-128
2b	d2i87b1	B:3-128

(no "CATH Domain" information available for 2I87)

(no "Pfam Domain" information available for 2I87)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DDL_STAAC | Q5HEB7)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008716	D-alanine-D-alanine ligase activity	Catalysis of the reaction: 2 D-alanine + ATP = D-alanyl-D-alanine + ADP + 2 H(+) + phosphate.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ile A:261 - Pro A:262	[ RasMol ]
		Ile B:261 - Pro B:262	[ RasMol ]
		Tyr A:172 - Pro A:173	[ RasMol ]
		Tyr B:172 - Pro B:173	[ RasMol ]

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	2i87
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UniProtKB/Swiss-Prot
	DDL_STAAC \| Q5HEB7	:	2i80 2i8c 3n8d

2i80	ALLOSTERIC INHIBITION OF STAPHYLOCOCCUS AUREUS D-ALANINE:D- ALANINE LIGASE REVEALED BY CRYSTALLOGRAPHIC STUDIES
2i8c	ALLOSTERIC INHIBITION OF STAPHYLOCOCCUS AUREUS D-ALANINE:D- ALANINE LIGASE REVEALED BY CRYSTALLOGRAPHIC STUDIES

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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Gene Ontology (12, 12)

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