Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1TWI

Crystal structure of Diaminopimelate Decarboxylase from m. jannaschii in co-complex with L-lysine

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0008652	biological_process	amino acid biosynthetic process
A	0008836	molecular_function	diaminopimelate decarboxylase activity
A	0009085	biological_process	lysine biosynthetic process
A	0009089	biological_process	lysine biosynthetic process via diaminopimelate
A	0016829	molecular_function	lyase activity
A	0016831	molecular_function	carboxy-lyase activity
A	0030170	molecular_function	pyridoxal phosphate binding
B	0003824	molecular_function	catalytic activity
B	0008652	biological_process	amino acid biosynthetic process
B	0008836	molecular_function	diaminopimelate decarboxylase activity
B	0009085	biological_process	lysine biosynthetic process
B	0009089	biological_process	lysine biosynthetic process via diaminopimelate
B	0016829	molecular_function	lyase activity
B	0016831	molecular_function	carboxy-lyase activity
B	0030170	molecular_function	pyridoxal phosphate binding
C	0003824	molecular_function	catalytic activity
C	0008652	biological_process	amino acid biosynthetic process
C	0008836	molecular_function	diaminopimelate decarboxylase activity
C	0009085	biological_process	lysine biosynthetic process
C	0009089	biological_process	lysine biosynthetic process via diaminopimelate
C	0016829	molecular_function	lyase activity
C	0016831	molecular_function	carboxy-lyase activity
C	0030170	molecular_function	pyridoxal phosphate binding
D	0003824	molecular_function	catalytic activity
D	0008652	biological_process	amino acid biosynthetic process
D	0008836	molecular_function	diaminopimelate decarboxylase activity
D	0009085	biological_process	lysine biosynthetic process
D	0009089	biological_process	lysine biosynthetic process via diaminopimelate
D	0016829	molecular_function	lyase activity
D	0016831	molecular_function	carboxy-lyase activity
D	0030170	molecular_function	pyridoxal phosphate binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 1607

Chain	Residue
C	HOH1688
C	HOH1711
C	HOH1728
C	HOH1729
C	HOH1842

site_id	AC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE LYS D 1601

Chain	Residue
A	TYR401
A	PLP1501
B	GLU373
B	TYR409
D	HOH1764
D	HOH1876
D	HOH1937
A	SER227
A	ARG307
A	ARG343
A	TYR347

site_id	AC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE LYS D 1602

Chain	Residue
A	CYS372
A	GLU373
A	TYR409
B	ARG307
B	ARG343
B	TYR347
B	TYR401
B	MET405
B	PLP1502
B	HOH1782
D	HOH1815

site_id	AC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE LYS D 1603

Chain	Residue
C	SER227
C	ARG307
C	ARG343
C	TYR347
C	TYR401
C	MET405
C	PLP1503
D	CYS372
D	GLU373
D	TYR409

site_id	AC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE LYS D 1604

Chain	Residue
C	ARG172
C	ASN192
C	PHE194
C	HIS224
C	ILE225
C	SER227
D	HOH1966
D	HOH1984

site_id	AC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE LYS D 1605

Chain	Residue
C	GLU373
C	TYR409
D	SER227
D	ARG307
D	ARG343
D	TYR347
D	TYR401
D	MET405
D	PLP1504
D	LYS1606
D	HOH1850

site_id	AC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE LYS D 1606

Chain	Residue
C	SER374
D	ARG172
D	ASN192
D	PHE194
D	HIS224
D	ILE225
D	GLY226
D	SER227
D	LYS1605
D	HOH1897
D	HOH1955
D	HOH1965

site_id	AC8
Number of Residues	16
Details	BINDING SITE FOR RESIDUE PLP A 1501

Chain	Residue
A	ALA81
A	LYS83
A	ASP102
A	ASN125
A	HIS224
A	SER227
A	GLY264
A	GLU304
A	GLY306
A	ARG307
A	TYR401
A	HOH1505
A	HOH1525
A	HOH1538
B	CYS372
D	LYS1601

site_id	AC9
Number of Residues	17
Details	BINDING SITE FOR RESIDUE PLP B 1502

Chain	Residue
B	HOH1785
D	LYS1602
A	CYS372
B	ALA81
B	LYS83
B	ASP102
B	ASN125
B	HIS224
B	SER227
B	GLY264
B	GLU304
B	GLY306
B	ARG307
B	TYR401
B	HOH1512
B	HOH1526
B	HOH1553

site_id	BC1
Number of Residues	16
Details	BINDING SITE FOR RESIDUE PLP C 1503

Chain	Residue
C	ALA81
C	LYS83
C	ASP102
C	HIS224
C	SER227
C	GLY264
C	GLU304
C	GLY306
C	ARG307
C	TYR401
C	HOH1609
C	HOH1630
C	HOH1641
C	HOH1716
D	CYS372
D	LYS1603

site_id	BC2
Number of Residues	17
Details	BINDING SITE FOR RESIDUE PLP D 1504

Chain	Residue
C	CYS372
D	ALA81
D	LYS83
D	ASP102
D	ASN125
D	HIS224
D	SER227
D	GLY264
D	GLU304
D	GLY306
D	ARG307
D	TYR401
D	LYS1605
D	HOH1627
D	HOH1632
D	HOH1645
D	HOH1731

Functional Information from PROSITE/UniProt

site_id	PS00878
Number of Residues	19
Details	ODR_DC_2_1 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. YAyKANanlaITrlLaklG

Chain	Residue	Details
A	TYR80-GLY98

site_id	PS00879
Number of Residues	14
Details	ODR_DC_2_2 Orn/DAP/Arg decarboxylases family 2 signature 2. Gie....IeDVNLGGGLG

Chain	Residue	Details
A	GLY253-GLY266

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Proton donor","evidences":[{"source":"HAMAP-Rule","id":"MF_02120","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12429091","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_02120","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"12429091","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12429091","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_02120","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Modified residue: {"description":"N6-(pyridoxal phosphate)lysine","evidences":[{"source":"PubMed","id":"12429091","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1bd0

Chain	Residue	Details
A	LYS83
A	LYS193

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 1bd0

Chain	Residue	Details
B	LYS83
B	LYS193

site_id	CSA3
Number of Residues	2
Details	Annotated By Reference To The Literature 1bd0

Chain	Residue	Details
C	LYS83
C	LYS193

site_id	CSA4
Number of Residues	2
Details	Annotated By Reference To The Literature 1bd0

Chain	Residue	Details
D	LYS83
D	LYS193

site_id	CSA5
Number of Residues	3
Details	Annotated By Reference To The Literature 1bd0

Chain	Residue	Details
A	GLU304
A	HIS224
A	LYS83

site_id	CSA6
Number of Residues	3
Details	Annotated By Reference To The Literature 1bd0

Chain	Residue	Details
B	GLU304
B	HIS224
B	LYS83

site_id	CSA7
Number of Residues	3
Details	Annotated By Reference To The Literature 1bd0

Chain	Residue	Details
C	GLU304
C	HIS224
C	LYS83

site_id	CSA8
Number of Residues	3
Details	Annotated By Reference To The Literature 1bd0

Chain	Residue	Details
D	GLU304
D	HIS224
D	LYS83

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