5C1O

Crystal structure of AMP-PNP complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0008360	biological_process	regulation of cell shape
A	0008716	molecular_function	D-alanine-D-alanine ligase activity
A	0009252	biological_process	peptidoglycan biosynthetic process
A	0016874	molecular_function	ligase activity
A	0046872	molecular_function	metal ion binding
A	0071555	biological_process	cell wall organization
B	0000166	molecular_function	nucleotide binding
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0008360	biological_process	regulation of cell shape
B	0008716	molecular_function	D-alanine-D-alanine ligase activity
B	0009252	biological_process	peptidoglycan biosynthetic process
B	0016874	molecular_function	ligase activity
B	0046872	molecular_function	metal ion binding
B	0071555	biological_process	cell wall organization
C	0000166	molecular_function	nucleotide binding
C	0005524	molecular_function	ATP binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0008360	biological_process	regulation of cell shape
C	0008716	molecular_function	D-alanine-D-alanine ligase activity
C	0009252	biological_process	peptidoglycan biosynthetic process
C	0016874	molecular_function	ligase activity
C	0046872	molecular_function	metal ion binding
C	0071555	biological_process	cell wall organization
D	0000166	molecular_function	nucleotide binding
D	0005524	molecular_function	ATP binding
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0008360	biological_process	regulation of cell shape
D	0008716	molecular_function	D-alanine-D-alanine ligase activity
D	0009252	biological_process	peptidoglycan biosynthetic process
D	0016874	molecular_function	ligase activity
D	0046872	molecular_function	metal ion binding
D	0071555	biological_process	cell wall organization

Functional Information from PDB Data

site_id	AC1
Number of Residues	15
Details	binding site for residue ANP A 401

Chain	Residue
A	LYS97
A	TYR210
A	TYR212
A	MET259
A	LEU269
A	GLU270
A	MG403
A	ILE142
A	LYS144
A	MET154
A	GLU180
A	LYS181
A	TRP182
A	LEU183
A	GLU187

---

site_id	AC2
Number of Residues	6
Details	binding site for residue NA A 402

Chain	Residue
A	GLU68
A	SER91
A	THR94
A	MET95
A	THR273
A	HOH504

---

site_id	AC3
Number of Residues	2
Details	binding site for residue MG A 403

Chain	Residue
A	GLU270
A	ANP401

---

site_id	AC4
Number of Residues	12
Details	binding site for residue ANP B 401

Chain	Residue
B	LYS97
B	LYS144
B	GLU148
B	SER151
B	MET154
B	GLU180
B	LYS181
B	LEU183
B	GLU187
B	MET259
B	GLU270
B	MG403

---

site_id	AC5
Number of Residues	6
Details	binding site for residue NA B 402

Chain	Residue
B	GLU68
B	SER91
B	THR94
B	MET95
B	THR273
B	HOH505

---

site_id	AC6
Number of Residues	4
Details	binding site for residue MG B 403

Chain	Residue
B	LYS97
B	GLU148
B	GLU270
B	ANP401

---

site_id	AC7
Number of Residues	2
Details	binding site for residue NA B 404

Chain	Residue
B	HIS265
C	HIS280

---

site_id	AC8
Number of Residues	17
Details	binding site for residue ANP C 401

Chain	Residue
C	LYS97
C	ILE142
C	LYS144
C	GLU148
C	SER151
C	MET154
C	GLU180
C	LYS181
C	TRP182
C	LEU183
C	GLU187
C	PHE209
C	TYR210
C	LYS215
C	MET259
C	GLU270
C	MG403

---

site_id	AC9
Number of Residues	6
Details	binding site for residue NA C 402

Chain	Residue
C	GLU68
C	SER91
C	THR94
C	MET95
C	THR273
C	HOH507

---

site_id	AD1
Number of Residues	3
Details	binding site for residue MG C 403

Chain	Residue
C	GLU148
C	GLU270
C	ANP401

---

site_id	AD2
Number of Residues	15
Details	binding site for residue ANP D 401

Chain	Residue
D	LYS97
D	ILE142
D	LYS144
D	GLU148
D	SER151
D	MET154
D	GLU180
D	LYS181
D	TRP182
D	LEU183
D	GLU187
D	PHE209
D	MET259
D	GLU270
D	MG403

---

site_id	AD3
Number of Residues	5
Details	binding site for residue NA D 402

Chain	Residue
D	GLU68
D	SER91
D	THR94
D	MET95
D	THR273

---

site_id	AD4
Number of Residues	3
Details	binding site for residue MG D 403

Chain	Residue
D	GLU148
D	GLU270
D	ANP401

---

Functional Information from PROSITE/UniProt

site_id	PS00843
Number of Residues	12
Details	DALA_DALA_LIGASE_1 D-alanine--D-alanine ligase signature 1. HGrgGEDGtLQG

Chain	Residue	Details
A	HIS63-GLY74

---

site_id	PS00844
Number of Residues	29
Details	DALA_DALA_LIGASE_2 D-alanine--D-alanine ligase signature 2. LdcsGwGRVDVMqdrdghfy....LlEVNTsPG

Chain	Residue	Details
A	LEU248-GLY276

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	67
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00047","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	202
Details	Domain: {"description":"ATP-grasp","evidences":[{"source":"HAMAP-Rule","id":"MF_00047","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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