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Title :   CRYSTAL STRUCTURE OF AMP-PNP COMPLEXED D-ALANINE-D-ALANINE LIGASE(DDL) FROM YERSINIA PESTIS

Authors :   H. T. Tran, L. W. Kang, M. K. Hong

Date :   15 Jun 15 (Deposition) - 02 Mar 16 (Release) - 02 Mar 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   D-Alanine-D-Alanine Ligase, Ddl, Drug Target, Bacterial Cell Wall Synthesis, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. T. Tran, M. K. Hong, H. P. Ngo, K. H. Huynh, Y. J. Ahn, Z. Wang, L. W. Kang
Structure Of D-Alanine-D-Alanine Ligase From Yersinia Pestis: Nucleotide Phosphate Recognition By The Serine Loop
Acta Crystallogr D Struct V. 72 12 2016 Biol
PubMed-ID: 26894530 | Reference-DOI: 10.1107/S2059798315021671

Molecule 1 - D-ALANINE--D-ALANINE LIGASE
	Chains	:	A, B, C, D
	EC Number	:	6.3.2.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	DDL, DDLB, YPO0557, Y3624, YP_3627
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632
	Synonym	:	D-ALA-D-ALA LIGASE,D-ALANYLALANINE SYNTHETASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 13)

No.	Name	Count	Type	Full Name
1	ANP	4	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	NA	5	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:97 , ILE A:142 , LYS A:144 , MET A:154 , GLU A:180 , LYS A:181 , TRP A:182 , LEU A:183 , GLU A:187 , TYR A:210 , TYR A:212 , MET A:259 , LEU A:269 , GLU A:270 , MG A:403	binding site for residue ANP A 401
02	AC2	SOFTWARE	GLU A:68 , SER A:91 , THR A:94 , MET A:95 , THR A:273 , HOH A:504	binding site for residue NA A 402
03	AC3	SOFTWARE	GLU A:270 , ANP A:401	binding site for residue MG A 403
04	AC4	SOFTWARE	LYS B:97 , LYS B:144 , GLU B:148 , SER B:151 , MET B:154 , GLU B:180 , LYS B:181 , LEU B:183 , GLU B:187 , MET B:259 , GLU B:270 , MG B:403	binding site for residue ANP B 401
05	AC5	SOFTWARE	GLU B:68 , SER B:91 , THR B:94 , MET B:95 , THR B:273 , HOH B:505	binding site for residue NA B 402
06	AC6	SOFTWARE	LYS B:97 , GLU B:148 , GLU B:270 , ANP B:401	binding site for residue MG B 403
07	AC7	SOFTWARE	HIS B:265 , HIS C:280	binding site for residue NA B 404
08	AC8	SOFTWARE	LYS C:97 , ILE C:142 , LYS C:144 , GLU C:148 , SER C:151 , MET C:154 , GLU C:180 , LYS C:181 , TRP C:182 , LEU C:183 , GLU C:187 , PHE C:209 , TYR C:210 , LYS C:215 , MET C:259 , GLU C:270 , MG C:403	binding site for residue ANP C 401
09	AC9	SOFTWARE	GLU C:68 , SER C:91 , THR C:94 , MET C:95 , THR C:273 , HOH C:507	binding site for residue NA C 402
10	AD1	SOFTWARE	GLU C:148 , GLU C:270 , ANP C:401	binding site for residue MG C 403
11	AD2	SOFTWARE	LYS D:97 , ILE D:142 , LYS D:144 , GLU D:148 , SER D:151 , MET D:154 , GLU D:180 , LYS D:181 , TRP D:182 , LEU D:183 , GLU D:187 , PHE D:209 , MET D:259 , GLU D:270 , MG D:403	binding site for residue ANP D 401
12	AD3	SOFTWARE	GLU D:68 , SER D:91 , THR D:94 , MET D:95 , THR D:273	binding site for residue NA D 402
13	AD4	SOFTWARE	GLU D:148 , GLU D:270 , ANP D:401	binding site for residue MG D 403

(no "SS Bond" information available for 5C1O)

Asymmetric Unit

No.	Residues
1	Leu A:139	-	Pro A:140
2	Gly A:185	-	Pro A:186
3	Cys A:225	-	Pro A:226
4	Leu B:139	-	Pro B:140
5	Gly B:185	-	Pro B:186
6	Cys B:225	-	Pro B:226
7	Leu C:139	-	Pro C:140
8	Gly C:185	-	Pro C:186
9	Cys C:225	-	Pro C:226
10	Leu D:139	-	Pro D:140
11	Gly D:185	-	Pro D:186
12	Cys D:225	-	Pro D:226

(no "SAP(SNP)/Variant" information available for 5C1O)

(no "PROSITE Motif" information available for 5C1O)

(no "Exon" information available for 5C1O)

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
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Chain A from PDB  Type:PROTEIN  Length:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee....hhhhh......eeee.........hhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhh......eeeeehhhhhh.hhhhhhhhhhh....eeeee.....eee.hhhhhhhhhhhhh....eeeeee.....eeeeeee..ee...eeee............eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c1o A   1 MAEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLKEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTKLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHVGMSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSIRIQPPGVFYDYSDKTQYFCPSGLSDESEQQLAALALQAYHALDCSGWGRVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILMLAD 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      |154       164       174       184       194       204       219       229       239       249       259       269       279       289       299       
                                                                                                                                                                            147|                                                         212|                                                                                        
                                                                                                                                                                             152                                                          218

Chain B from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee...............eeee.........hhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhh..eeeee.......eee.hhhhhhhhhhhhhh...eeeeee.....eeeeeee..ee...eeee...eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee........hhhhhhhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c1o B   1 MAEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLKEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTKLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHESVGMSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSIRIQPPTQYFCPSGLSDESEQQLAALALQAYHALDCSGWGRVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILMLAD 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       152       162       172       182       192       202   ||  226       236       246       256       266       276       286       296       306
                                                                                                                                                                             148|                                                    206|                                                                                     
                                                                                                                                                                              151                                                     221

Chain C from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhhhhh...eeeee....hhhhh......eeee.........hhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhh..eeeee.........eee.hhhhhhhhhhhhhhh..eeeeee.....eeeeeee..ee...eeee......hhhhhhh....eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee........hhhhhhhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5c1o C   1 MAEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLKEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTKLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHEGSSVGMSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSIRIQPPGVFYDYDAKYLSDKTQYFCPSGLSDESEQQLAALALQAYHALDCSGWGRVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILMLAD 306
                                    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

Chain D from PDB  Type:PROTEIN  Length:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhhhhh...eeeee....hhhhh......eeee.........hhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhh..eeeee.......eee.hhhhhhhhhhhhh....eeeeee.....eeeeeee..ee...eeee........eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee........hhhhhhhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c1o D   1 MAEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLKEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTKLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHESVGMSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSIRIQPPGVFDKTQYFCPSGLSDESEQQLAALALQAYHALDCSGWGRVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILMLAD 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       152       162       172       182       192       202      |221       231       241       251       261       271       281       291       301     
                                                                                                                                                                             148|                                                       209|                                                                                       
                                                                                                                                                                              151                                                        219

Legend:		→ Mismatch	(orange background)
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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 '\|'

(no "SCOP Domain" information available for 5C1O)

(no "CATH Domain" information available for 5C1O)

(no "Pfam Domain" information available for 5C1O)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Cys A:225 - Pro A:226	[ RasMol ]
		Cys B:225 - Pro B:226	[ RasMol ]
		Cys C:225 - Pro C:226	[ RasMol ]
		Cys D:225 - Pro D:226	[ RasMol ]
		Gly A:185 - Pro A:186	[ RasMol ]
		Gly B:185 - Pro B:186	[ RasMol ]
		Gly C:185 - Pro C:186	[ RasMol ]
		Gly D:185 - Pro D:186	[ RasMol ]
		Leu A:139 - Pro A:140	[ RasMol ]
		Leu B:139 - Pro B:140	[ RasMol ]
		Leu C:139 - Pro C:140	[ RasMol ]
		Leu D:139 - Pro D:140	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

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