Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3PB2

Characterisation of the first monomeric dihydrodipicolinate synthase variant reveals evolutionary insights

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
A	0009085	biological_process	lysine biosynthetic process
A	0009089	biological_process	lysine biosynthetic process via diaminopimelate
A	0016829	molecular_function	lyase activity
A	0019877	biological_process	diaminopimelate biosynthetic process
A	0044281	biological_process	small molecule metabolic process
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
B	0009085	biological_process	lysine biosynthetic process
B	0009089	biological_process	lysine biosynthetic process via diaminopimelate
B	0016829	molecular_function	lyase activity
B	0019877	biological_process	diaminopimelate biosynthetic process
B	0044281	biological_process	small molecule metabolic process
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
C	0009085	biological_process	lysine biosynthetic process
C	0009089	biological_process	lysine biosynthetic process via diaminopimelate
C	0016829	molecular_function	lyase activity
C	0019877	biological_process	diaminopimelate biosynthetic process
C	0044281	biological_process	small molecule metabolic process
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
D	0009085	biological_process	lysine biosynthetic process
D	0009089	biological_process	lysine biosynthetic process via diaminopimelate
D	0016829	molecular_function	lyase activity
D	0019877	biological_process	diaminopimelate biosynthetic process
D	0044281	biological_process	small molecule metabolic process
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
E	0009085	biological_process	lysine biosynthetic process
E	0009089	biological_process	lysine biosynthetic process via diaminopimelate
E	0016829	molecular_function	lyase activity
E	0019877	biological_process	diaminopimelate biosynthetic process
E	0044281	biological_process	small molecule metabolic process
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
F	0009085	biological_process	lysine biosynthetic process
F	0009089	biological_process	lysine biosynthetic process via diaminopimelate
F	0016829	molecular_function	lyase activity
F	0019877	biological_process	diaminopimelate biosynthetic process
F	0044281	biological_process	small molecule metabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 295

Chain	Residue
A	TYR120
A	HOH383
B	GLU17
B	LEU271
B	HOH340
B	HOH487

site_id	AC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL A 296

Chain	Residue
A	ARG124
A	HOH340
A	HOH410
B	LYS14
B	HOH487
A	LYS119
A	TYR120
A	GLU123

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 297

Chain	Residue
A	VAL134
A	ARG137
A	GLY189
A	PHE247
A	ASN251
A	HOH391
A	HOH717

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A 298

Chain	Residue
A	TYR224
A	GLY227
C	ARG28
E	GLU230

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 299

Chain	Residue
A	PRO135
A	VAL140
A	ASN141
A	HOH406
A	HOH485
A	HOH936

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 300

Chain	Residue
A	ALA200
A	HOH452
A	HOH461
A	HOH688
A	HOH897
A	HOH1012

site_id	AC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL B 295

Chain	Residue
B	TYR132
B	ARG137
B	ALA163
B	GLY189
B	PHE247
B	ASN251
B	HOH787
B	HOH1003
B	HOH1063

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL B 296

Chain	Residue
B	GLU32
B	LYS215
B	GLU223

site_id	AC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL B 297

Chain	Residue
A	TYR106
A	HOH368
B	SER47
B	PRO48
B	GLY77
B	HOH755
B	HOH861

site_id	BC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL B 298

Chain	Residue
A	TYR120
A	ARG124
A	HOH326
A	HOH428
A	HOH745
B	GLU17
B	LEU18
B	LYS57
B	HOH604

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL C 295

Chain	Residue
C	TYR224
C	GLY227
C	LEU229

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL C 296

Chain	Residue
C	TYR132
C	ARG137
C	LYS161
C	GLY189
C	PHE247
C	ASN251
C	HOH727

site_id	BC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL C 297

Chain	Residue
C	GLY4
C	VAL5
C	ASN36
C	VAL218
C	CYS221
C	ALA222
C	PHE225
C	HOH412
C	HOH785

site_id	BC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL C 298

Chain	Residue
C	TYR29
C	ALA213
C	PRO214
C	LYS215
C	GLN216
C	LEU293
C	HOH334
C	HOH856
C	HOH860

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL D 295

Chain	Residue
D	LYS108
D	PRO109
D	THR110
D	GLN111
D	THR250

Functional Information from PROSITE/UniProt

site_id	PS00665
Number of Residues	18
Details	DHDPS_1 Dihydrodipicolinate synthase signature 1. ALIvlGTTGESptvnedE

Chain	Residue	Details
A	ALA37-GLU54

site_id	PS00666
Number of Residues	32
Details	DHDPS_2 Dihydrodipicolinate synthase signature 2. YNVPgrTgvnVlpetaariaadlknVvGIKEA

Chain	Residue	Details
A	TYR132-ALA163

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	ACT_SITE: Proton donor/acceptor => ECO:0000255\|HAMAP-Rule:MF_00418

Chain	Residue	Details
A	TYR132
B	TYR132
C	TYR132
D	TYR132
E	TYR132
F	TYR132

site_id	SWS_FT_FI2
Number of Residues	6
Details	ACT_SITE: Schiff-base intermediate with substrate => ECO:0000255\|HAMAP-Rule:MF_00418

Chain	Residue	Details
A	LYS161
B	LYS161
C	LYS161
D	LYS161
E	LYS161
F	LYS161

site_id	SWS_FT_FI3
Number of Residues	12
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00418

Chain	Residue	Details
A	THR44
E	ILE206
F	THR44
F	ILE206
A	ILE206
B	THR44
B	ILE206
C	THR44
C	ILE206
D	THR44
D	ILE206
E	THR44

site_id	SWS_FT_FI4
Number of Residues	12
Details	SITE: Part of a proton relay during catalysis => ECO:0000255\|HAMAP-Rule:MF_00418

Chain	Residue	Details
A	THR43
E	TYR106
F	THR43
F	TYR106
A	TYR106
B	THR43
B	TYR106
C	THR43
C	TYR106
D	THR43
D	TYR106
E	THR43

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)