Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6U01

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84D mutant with pyruvate bound in the active site

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0008700	molecular_function	4-hydroxy-2-oxoglutarate aldolase activity
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	0009436	biological_process	glyoxylate catabolic process
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	0008700	molecular_function	4-hydroxy-2-oxoglutarate aldolase activity
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	0009436	biological_process	glyoxylate catabolic process
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	0008700	molecular_function	4-hydroxy-2-oxoglutarate aldolase activity
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	0009436	biological_process	glyoxylate catabolic process
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	0008700	molecular_function	4-hydroxy-2-oxoglutarate aldolase activity
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	0009436	biological_process	glyoxylate catabolic process
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	0008700	molecular_function	4-hydroxy-2-oxoglutarate aldolase activity
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	0009436	biological_process	glyoxylate catabolic process
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	0008700	molecular_function	4-hydroxy-2-oxoglutarate aldolase activity
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	0009436	biological_process	glyoxylate catabolic process
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	3
Details	binding site for residue EDO A 301

Chain	Residue
A	ARG142
A	PHE248
A	ASN252

site_id	AC2
Number of Residues	4
Details	binding site for residue PG4 A 302

Chain	Residue
A	GLN117
A	ASP150
A	THR151
A	LYS154

site_id	AC3
Number of Residues	6
Details	binding site for residue MG B 301

Chain	Residue
A	HOH511
B	HOH402
B	HOH436
B	HOH445
A	ASP227
A	HOH440

site_id	AC4
Number of Residues	6
Details	binding site for residue MG B 302

Chain	Residue
A	HOH442
A	HOH452
A	HOH481
B	ASP227
B	HOH455
B	HOH471

site_id	AC5
Number of Residues	6
Details	binding site for residue MG B 303

Chain	Residue
B	SER189
B	GLU191
B	ASP192
B	ASN195
B	ILE207
B	EDO305

site_id	AC6
Number of Residues	6
Details	binding site for residue EDO B 304

Chain	Residue
A	TYR196
A	LYS231
A	LYS234
B	SER200
B	GLU228
B	TYR230

site_id	AC7
Number of Residues	7
Details	binding site for residue EDO B 305

Chain	Residue
B	GLY190
B	GLU191
B	ASP192
B	ILE207
B	VAL209
B	PHE248
B	MG303

site_id	AC8
Number of Residues	2
Details	binding site for residue EDO B 306

Chain	Residue
B	ASP177
B	HIS181

site_id	AC9
Number of Residues	4
Details	binding site for residue PGE B 307

Chain	Residue
B	GLN117
B	ASP150
B	THR151
B	LYS154

site_id	AD1
Number of Residues	1
Details	binding site for residue ACT B 308

Chain	Residue
B	PHE298

site_id	AD2
Number of Residues	1
Details	binding site for residue MG C 301

Chain	Residue
C	ASP158

site_id	AD3
Number of Residues	9
Details	binding site for residue EDO C 302

Chain	Residue
C	KPI166
C	GLY190
C	GLU191
C	ASP192
C	ILE207
C	VAL209
C	PHE248
C	HOH469
C	HOH478

site_id	AD4
Number of Residues	4
Details	binding site for residue PGE C 303

Chain	Residue
C	GLN117
C	ASP150
C	THR151
C	LYS154

site_id	AD5
Number of Residues	2
Details	binding site for residue ACT C 304

Chain	Residue
C	PHE156
C	ARG184

site_id	AD6
Number of Residues	2
Details	binding site for residue ACT C 305

Chain	Residue
B	THR55
C	HIS87

site_id	AD7
Number of Residues	3
Details	binding site for residue ACT C 306

Chain	Residue
C	ASP150
C	ASP177
C	HOH491

site_id	AD8
Number of Residues	5
Details	binding site for residue PGE D 301

Chain	Residue
D	GLN117
D	TYR120
D	ASP150
D	THR151
D	LYS154

site_id	AD9
Number of Residues	3
Details	binding site for residue ACT D 302

Chain	Residue
D	ARG142
D	KPI166
D	ASN252

site_id	AE1
Number of Residues	7
Details	binding site for residue EDO E 301

Chain	Residue
E	ASP238
E	GLU239
E	TYR241
E	ASN242
E	TYR293
E	EDO302
F	HIS181

site_id	AE2
Number of Residues	6
Details	binding site for residue EDO E 302

Chain	Residue
E	GLU239
E	ASN242
E	LYS292
E	TYR293
E	EDO301
E	HOH407

site_id	AE3
Number of Residues	5
Details	binding site for residue PGE E 303

Chain	Residue
E	GLN117
E	TYR120
E	ASP150
E	THR151
E	LYS154

site_id	AE4
Number of Residues	8
Details	binding site for residue GOL E 304

Chain	Residue
E	HOH427
C	LYS32
C	LYS71
C	GLY72
E	LEU262
E	GLU287
E	MET290
E	LYS291

site_id	AE5
Number of Residues	3
Details	binding site for residue ACT E 305

Chain	Residue
E	ARG142
E	KPI166
E	ASN252

site_id	AE6
Number of Residues	5
Details	binding site for residue MG F 302

Chain	Residue
D	ASP40
D	HOH486
D	HOH519
F	HOH430
F	HOH459

site_id	AE7
Number of Residues	6
Details	binding site for residue EDO F 303

Chain	Residue
D	PHE224
F	GLN128
F	CYS159
F	HOH407
F	HOH413
F	HOH502

site_id	AE8
Number of Residues	5
Details	binding site for residue EDO F 304

Chain	Residue
F	TYR137
F	ARG142
F	KPI166
F	GLY190
F	ASN252

site_id	AE9
Number of Residues	3
Details	binding site for residue EDO F 305

Chain	Residue
F	SER279
F	ASN282
F	HOH442

site_id	AF1
Number of Residues	6
Details	binding site for residue EDO F 306

Chain	Residue
D	ASN37
D	HOH496
F	LYS3
F	ARG157
F	GLU160
F	HOH432

site_id	AF2
Number of Residues	5
Details	binding site for residue PEG F 307

Chain	Residue
D	LYS74
F	GLN117
F	TYR120
F	THR151
F	LYS154

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ALA41-GLU58

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

Chain	Residue	Details
A	TYR137-ALA168

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	TYR137
B	TYR137
C	TYR137
D	TYR137
E	TYR137
F	TYR137

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	KPI166
B	KPI166
C	KPI166
D	KPI166
E	KPI166
F	KPI166

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

Chain	Residue	Details
A	THR48
E	ILE207
F	THR48
F	ILE207
A	ILE207
B	THR48
B	ILE207
C	THR48
C	ILE207
D	THR48
D	ILE207
E	THR48

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	THR47
E	TYR111
F	THR47
F	TYR111
A	TYR111
B	THR47
B	TYR111
C	THR47
C	TYR111
D	THR47
D	TYR111
E	THR47

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