5C1P

Crystal structure of ADP and D-alanyl-D-alanine 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	6
Details	binding site for residue NA A 401

Chain	Residue
A	GLU68
A	SER91
A	THR94
A	MET95
A	THR273
A	HOH517

---

site_id	AC2
Number of Residues	4
Details	binding site for residue GOL A 402

Chain	Residue
A	GLY66
A	GLY11
A	THR12
A	THR42

---

site_id	AC3
Number of Residues	5
Details	binding site for residue GOL A 403

Chain	Residue
A	GLU77
A	GLN80
A	LEU81
A	TYR83
A	ASP306

---

site_id	AC4
Number of Residues	10
Details	binding site for residue ADP B 401

Chain	Residue
B	LYS97
B	ILE142
B	LYS144
B	GLU180
B	LYS181
B	LEU183
B	GLU187
B	TYR210
B	MET259
B	GLU270

---

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	HOH512

---

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

Chain	Residue
B	GLY11
B	THR12
B	THR42
B	GLY66

---

site_id	AC7
Number of Residues	15
Details	binding site for residue ADP C 401

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

---

site_id	AC8
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	HOH543

---

site_id	AC9
Number of Residues	7
Details	binding site for residue ACT C 403

Chain	Residue
C	ARG255
C	GLY276
C	SER281
C	LEU282
C	HOH501
C	HOH519
C	HOH533

---

site_id	AD1
Number of Residues	1
Details	binding site for residue GOL C 404

Chain	Residue
C	ALA247

---

site_id	AD2
Number of Residues	4
Details	binding site for residue GOL C 405

Chain	Residue
A	ASP306
C	GLN296
C	ARG300
C	HOH547

---

site_id	AD3
Number of Residues	5
Details	binding site for residue GOL C 406

Chain	Residue
C	LEU76
C	GLU77
C	LEU81
C	ASP306
C	GOL407

---

site_id	AD4
Number of Residues	6
Details	binding site for residue GOL C 407

Chain	Residue
C	PRO82
C	TYR83
C	GLY85
C	GLY87
C	ASP306
C	GOL406

---

site_id	AD5
Number of Residues	4
Details	binding site for residue NA C 408

Chain	Residue
A	HIS265
A	HOH507
C	HIS280
C	HOH575

---

site_id	AD6
Number of Residues	14
Details	binding site for residue ADP D 401

Chain	Residue
D	LYS97
D	ILE142
D	LYS144
D	GLU148
D	GLU180
D	LYS181
D	TRP182
D	LEU183
D	GLU187
D	PHE209
D	TYR210
D	MET259
D	GLU270
D	HOH527

---

site_id	AD7
Number of Residues	6
Details	binding site for residue NA D 404

Chain	Residue
D	THR94
D	MET95
D	THR273
D	HOH508
D	GLU68
D	SER91

---

site_id	AD8
Number of Residues	11
Details	binding site for Di-peptide DAL D 402 and DAL D 403

Chain	Residue
D	TYR210
D	LYS215
D	TYR216
D	ARG255
D	ASN272
D	PRO275
D	GLY276
D	SER281
D	LEU282
D	HOH505
D	HOH506

---

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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