Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3M5V

Crystal Structure of Dihydrodipicolinate Synthase from Campylobacter jejuni

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 A 301

Chain	Residue
A	ASN84
A	TYR110
A	HOH311
A	HOH1131
C	ASN84
C	TYR110
C	HOH347

site_id	AC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 A 302

Chain	Residue
A	SER251
A	ASN252
A	HOH496
A	HOH1071
A	HOH1144
C	LYS113
A	ARG142
A	PHE248

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 303

Chain	Residue
A	ASN229
A	TYR230
A	LYS231
A	GLU232

site_id	AC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL A 304

Chain	Residue
A	LYS280

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 305

Chain	Residue
A	THR115
A	GLN116
A	HOH328
A	HOH613

site_id	AC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 B 302

Chain	Residue
B	ARG142
B	PHE248
B	SER251
B	ASN252
B	HOH447
B	HOH884
B	HOH1125
B	HOH1127
D	LYS113

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL B 303

Chain	Residue
B	THR115
B	GLN116
B	HOH1098
D	HOH333

site_id	AC8
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PEG B 305

Chain	Residue
B	GLY46
B	THR47
B	ALA81
B	GLY82
B	LEU105
B	VAL107
B	TYR137
B	LYS166
B	HOH631
B	HOH1136
B	HOH1151

site_id	AC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL B 306

Chain	Residue
B	ASN242

site_id	BC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL C 301

Chain	Residue
C	LYS280

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL C 302

Chain	Residue
A	HOH584
C	THR115
C	GLN116
C	HOH1072
C	HOH1105

site_id	BC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL C 303

Chain	Residue
C	SER277

site_id	BC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 304

Chain	Residue
A	LYS113
C	ARG142
C	PHE248
C	SER251
C	ASN252
C	HOH365
C	HOH1152
C	HOH1154

site_id	BC5
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PEG C 305

Chain	Residue
C	GLY46
C	THR47
C	ALA81
C	GLY82
C	LEU105
C	SER106
C	VAL107
C	TYR137
C	LYS166
C	HOH440
C	HOH1132
C	HOH1156

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 D 301

Chain	Residue
B	ASN84
B	TYR110
D	ASN84
D	TYR110
D	HOH382

site_id	BC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 D 299

Chain	Residue
D	ASN229
D	TYR230
D	LYS231
D	GLU232
D	HOH509

site_id	BC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL D 302

Chain	Residue
D	LYS280

site_id	BC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL D 303

Chain	Residue
D	ARG60

site_id	CC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL D 304

Chain	Residue
B	HOH453
D	THR115
D	GLN116
D	HOH1084

site_id	CC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 D 305

Chain	Residue
D	HOH628
B	LYS113
D	ARG142
D	PHE248
D	SER251
D	ASN252
D	HOH409
D	HOH615

site_id	CC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PEG D 306

Chain	Residue
D	GLY46
D	THR47
D	GLY82
D	LEU105
D	SER106
D	VAL107
D	TYR137
D	LYS166
D	HOH448
D	HOH522
D	HOH1157

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	4
Details	ACT_SITE: Proton donor/acceptor => ECO:0000255\|HAMAP-Rule:MF_00418

Chain	Residue	Details
A	TYR137
B	TYR137
C	TYR137
D	TYR137

site_id	SWS_FT_FI2
Number of Residues	4
Details	ACT_SITE: Schiff-base intermediate with substrate => ECO:0000255\|HAMAP-Rule:MF_00418

Chain	Residue	Details
A	LYS166
B	LYS166
C	LYS166
D	LYS166

site_id	SWS_FT_FI3
Number of Residues	8
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00418

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

site_id	SWS_FT_FI4
Number of Residues	8
Details	SITE: Part of a proton relay during catalysis => ECO:0000255\|HAMAP-Rule:MF_00418

Chain	Residue	Details
A	THR47
A	TYR111
B	THR47
B	TYR111
C	THR47
C	TYR111
D	THR47
D	TYR111

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