Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1XXX

Crystal structure of Dihydrodipicolinate Synthase (DapA, Rv2753c) from Mycobacterium tuberculosis

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0008652	biological_process	amino acid biosynthetic process
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	0005886	cellular_component	plasma membrane
B	0008652	biological_process	amino acid biosynthetic process
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	0005886	cellular_component	plasma membrane
C	0008652	biological_process	amino acid biosynthetic process
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	0005886	cellular_component	plasma membrane
D	0008652	biological_process	amino acid biosynthetic process
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	0005886	cellular_component	plasma membrane
E	0008652	biological_process	amino acid biosynthetic process
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	0005886	cellular_component	plasma membrane
F	0008652	biological_process	amino acid biosynthetic process
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
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0005886	cellular_component	plasma membrane
G	0008652	biological_process	amino acid biosynthetic process
G	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
G	0009085	biological_process	lysine biosynthetic process
G	0009089	biological_process	lysine biosynthetic process via diaminopimelate
G	0016829	molecular_function	lyase activity
G	0019877	biological_process	diaminopimelate biosynthetic process
G	0044281	biological_process	small molecule metabolic process
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0005886	cellular_component	plasma membrane
H	0008652	biological_process	amino acid biosynthetic process
H	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
H	0009085	biological_process	lysine biosynthetic process
H	0009089	biological_process	lysine biosynthetic process via diaminopimelate
H	0016829	molecular_function	lyase activity
H	0019877	biological_process	diaminopimelate biosynthetic process
H	0044281	biological_process	small molecule metabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 2001

Chain	Residue
A	ALA162
A	HIS164
A	ILE167
A	HOH3026
A	HOH3080
A	HOH3233

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 2002

Chain	Residue
B	HOH3072
B	HOH3232
B	ALA162
B	HIS164
B	ILE167

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG C 2003

Chain	Residue
C	ALA162
C	HIS164
C	ILE167
C	HOH3160

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG D 2004

Chain	Residue
D	ALA162
D	HIS164
D	ILE167
D	HOH3090

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG E 2005

Chain	Residue
E	ALA162
E	HIS164
E	ILE167
E	HOH3038

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG F 2006

Chain	Residue
F	ALA162
F	HIS164
F	ILE167

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG G 2007

Chain	Residue
G	ALA162
G	HIS164
G	ILE167
G	HOH3147
G	HOH3226

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG H 2008

Chain	Residue
H	ALA162
H	HIS164
H	ILE167
H	HOH3095
H	HOH3184

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL A 2009

Chain	Residue
A	LYS174
A	SER179
A	HOH3122

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CL B 2010

Chain	Residue
B	PRO155
B	LYS174
B	SER179
B	ILE183
B	HOH3168
B	HOH3193

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL C 2011

Chain	Residue
C	LYS174
C	SER179
C	ILE183
C	HOH3024

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL D 2012

Chain	Residue
D	LYS174
D	SER179
D	ILE183
D	HOH3079

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL E 2013

Chain	Residue
E	PRO155
E	LYS174
E	SER179
E	ILE183

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL F 2014

Chain	Residue
F	LYS174
F	SER179
F	ILE183
F	HOH3032
F	HOH3048

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL G 2015

Chain	Residue
G	LYS174
G	SER179
G	ILE183

site_id	BC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL H 2016

Chain	Residue
H	LYS174
H	SER179
H	ILE183

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE DTT A 3001

Chain	Residue
A	ASP195
A	ALA197
A	CYS248
A	MET251
A	SER252
A	HOH3144

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE DTT B 3002

Chain	Residue
B	ASP195
B	ASP196
B	ALA197
B	CYS248
B	SER252

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE DTT C 3003

Chain	Residue
C	ASP195
C	ALA197
C	CYS248
C	MET251
C	SER252

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE DTT D 3004

Chain	Residue
D	ASP195
D	ASP196
D	ALA197
D	CYS248
D	SER252

site_id	CC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE DTT E 3005

Chain	Residue
E	ASP195
E	ASP196
E	ALA197
E	CYS248
E	SER252

site_id	CC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE DTT F 3006

Chain	Residue
F	ASP195
F	ALA197
F	CYS248
F	SER252

site_id	CC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE DTT G 3007

Chain	Residue
G	ALA197
G	CYS248
G	MET251
G	SER252
G	ASP195

site_id	CC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE DTT H 3008

Chain	Residue
H	ASP195
H	ALA197
H	CYS248
H	MET251
H	SER252
H	HOH3085

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	GLY48-GLU65

site_id	PS00666
Number of Residues	31
Details	DHDPS_2 Dihydrodipicolinate synthase signature 2. YDIPgrSavpIepdtiralashpn.IvGVKDA

Chain	Residue	Details
A	TYR143-ALA173

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Active site: {"description":"Proton donor/acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_00418","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	8
Details	Active site: {"description":"Schiff-base intermediate with substrate","evidences":[{"source":"HAMAP-Rule","id":"MF_00418","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21672512","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00418","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	16
Details	Site: {"description":"Part of a proton relay during catalysis","evidences":[{"source":"HAMAP-Rule","id":"MF_00418","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
A	TYR143
A	ARG148
A	LYS171

site_id	CSA10
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
B	THR54
B	LYS171
B	THR55

site_id	CSA11
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
C	THR54
C	LYS171
C	THR55

site_id	CSA12
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
D	THR54
D	LYS171
D	THR55

site_id	CSA13
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
E	THR54
E	LYS171
E	THR55

site_id	CSA14
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
F	THR54
F	LYS171
F	THR55

site_id	CSA15
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
G	THR54
G	LYS171
G	THR55

site_id	CSA16
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
H	THR54
H	LYS171
H	THR55

site_id	CSA2
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
B	TYR143
B	ARG148
B	LYS171

site_id	CSA3
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
C	TYR143
C	ARG148
C	LYS171

site_id	CSA4
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
D	TYR143
D	ARG148
D	LYS171

site_id	CSA5
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
E	TYR143
E	ARG148
E	LYS171

site_id	CSA6
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
F	TYR143
F	ARG148
F	LYS171

site_id	CSA7
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
G	TYR143
G	ARG148
G	LYS171

site_id	CSA8
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
H	TYR143
H	ARG148
H	LYS171

site_id	CSA9
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
A	THR54
A	LYS171
A	THR55

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)