Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4OE7

Crystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0016829	molecular_function	lyase activity
A	0042802	molecular_function	identical protein binding
A	0046176	biological_process	aldonic acid catabolic process
A	0047440	molecular_function	2-dehydro-3-deoxy-D-pentonate aldolase activity
A	0061677	molecular_function	2-dehydro-3-deoxy-D-gluconate aldolase activity
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0016829	molecular_function	lyase activity
B	0042802	molecular_function	identical protein binding
B	0046176	biological_process	aldonic acid catabolic process
B	0047440	molecular_function	2-dehydro-3-deoxy-D-pentonate aldolase activity
B	0061677	molecular_function	2-dehydro-3-deoxy-D-gluconate aldolase activity
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0016829	molecular_function	lyase activity
C	0042802	molecular_function	identical protein binding
C	0046176	biological_process	aldonic acid catabolic process
C	0047440	molecular_function	2-dehydro-3-deoxy-D-pentonate aldolase activity
C	0061677	molecular_function	2-dehydro-3-deoxy-D-gluconate aldolase activity
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0016829	molecular_function	lyase activity
D	0042802	molecular_function	identical protein binding
D	0046176	biological_process	aldonic acid catabolic process
D	0047440	molecular_function	2-dehydro-3-deoxy-D-pentonate aldolase activity
D	0061677	molecular_function	2-dehydro-3-deoxy-D-gluconate aldolase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO A 401

Chain	Residue
A	LEU54
A	PHE60
A	ARG68
A	GLY88
A	THR89
A	GLY90
A	VAL113
A	VAL114
A	ILE115

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 402

Chain	Residue
A	LYS69
A	ALA70
A	ARG73
A	HIS103
A	HOH522
D	ASP136

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 403

Chain	Residue
A	ASP49
A	VAL231
A	LEU234
A	LYS235
A	ARG238

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG A 404

Chain	Residue
A	GLY57
A	GXT409
A	PYR410

site_id	AC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO A 405

Chain	Residue
A	LEU54
A	ARG68
A	LYS69
A	ALA72
A	ILE87
A	LEU100
A	HIS103
A	ALA104
A	HOH507

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 406

Chain	Residue
A	THR92
A	PRO117
A	TYR118
A	TYR119
A	TRP120
B	GLN62
B	PRO287

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 407

Chain	Residue
A	ASP178
A	TYR203
A	ASP205
A	HIS206
C	ALA181
C	ARG184

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 408

Chain	Residue
A	THR156
A	PRO157
A	ALA158

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GXT A 409

Chain	Residue
A	SER56
A	PHE147
A	TYR203
A	MG404
A	PYR410
A	HOH529

site_id	BC1
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PYR A 410

Chain	Residue
A	PRO20
A	PHE52
A	GLY55
A	SER56
A	GLY57
A	TYR145
A	LYS174
A	GLY202
A	ILE219
A	MG404
A	GXT409
A	HOH529

site_id	BC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO B 401

Chain	Residue
B	LEU54
B	PHE60
B	ARG68
B	GLY88
B	THR89
B	GLY90
B	VAL113
B	VAL114
B	ILE115

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL B 402

Chain	Residue
B	GLY29
B	GLN30
B	LEU31
B	GLU67
C	ALA27

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL B 403

Chain	Residue
B	ALA181
B	HIS182
B	SER185
D	GLN260

site_id	BC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 404

Chain	Residue
B	LYS244
B	GLY247
B	TYR248

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 405

Chain	Residue
B	PRO20
B	GLY57
B	GXP410
B	GXS411
B	HOH512

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 406

Chain	Residue
B	PHE147
B	ALA149
B	ILE177
B	ASP178
B	TYR203
B	HOH520

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 407

Chain	Residue
B	ALA65
B	GLU66
B	GLU67
B	GLY64

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 408

Chain	Residue
A	ARG95
B	GLY29
B	HIS283
B	LEU285
B	PRO286

site_id	CC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO B 409

Chain	Residue
A	GLN62
A	PRO287
B	THR92
B	PRO117
B	TYR118
B	TYR119
B	TRP120

site_id	CC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GXP B 410

Chain	Residue
B	PRO20
B	PHE52
B	GLY55
B	SER56
B	GLY57
B	TYR145
B	PHE147
B	LYS174
B	THR176
B	GLY202
B	MG405

site_id	CC3
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GXS B 411

Chain	Residue
B	PRO20
B	PHE52
B	GLY55
B	SER56
B	GLY57
B	TYR145
B	PHE147
B	LYS174
B	THR176
B	GLY202
B	MG405
B	HOH523

site_id	CC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE EDO C 401

Chain	Residue
C	LEU54
C	PHE60
C	ARG68
C	GLY88
C	THR89
C	GLY90
C	VAL113
C	VAL114
C	ILE115
C	TYR145

site_id	CC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL C 402

Chain	Residue
C	ASP49
C	VAL231
C	LEU234
C	LYS235
C	ARG238
C	HOH540

site_id	CC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG C 403

Chain	Residue
C	GLY57
C	PYR412

site_id	CC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO C 404

Chain	Residue
C	LEU54
C	ARG68
C	LYS69
C	ALA72
C	ILE87
C	LEU100
C	HIS103
C	ALA104
C	HOH517

site_id	CC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 405

Chain	Residue
C	THR156
C	PRO157
C	ALA158

site_id	CC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 406

Chain	Residue
A	ALA181
A	ARG184
C	ASP178
C	TYR203
C	ASP205
C	HIS206

site_id	DC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 407

Chain	Residue
C	ILE24
C	ASP32
C	GLY35
C	PRO279
C	VAL280
C	SER281

site_id	DC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 408

Chain	Residue
C	ILE177
C	ASP178
C	TYR203

site_id	DC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 409

Chain	Residue
A	GLN260
C	ALA181
C	ARG184

site_id	DC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 410

Chain	Residue
C	GLY152
C	GLN153
C	ASP154

site_id	DC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 411

Chain	Residue
C	PRO286
C	PRO287
D	ASN126
D	ARG129
D	TYR130
D	GLN133

site_id	DC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PYR C 412

Chain	Residue
C	PRO20
C	PHE52
C	GLY55
C	SER56
C	GLY57
C	TYR145
C	LYS174
C	GLY202
C	ILE219
C	MG403
C	HOH527

site_id	DC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE EDO C 413

Chain	Residue
C	LYS121
C	LEU150
C	THR151
C	GLY152
C	HOH541
C	HOH544
D	LYS121
D	PRO148
D	ALA149
D	GLY152

site_id	DC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 401

Chain	Residue
B	ALA181
B	ARG184
D	ASP178
D	TYR203
D	ASP205
D	HIS206
D	PRO256

site_id	DC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO D 402

Chain	Residue
D	LEU54
D	PHE60
D	ARG68
D	GLY88
D	THR89
D	GLY90
D	VAL113
D	VAL114
D	ILE115

site_id	EC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 403

Chain	Residue
D	THR156
D	PRO157
D	ALA158

site_id	EC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO D 404

Chain	Residue
D	ASP42
D	ASN224
D	PRO227
D	ARG278

site_id	EC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL D 405

Chain	Residue
D	GLN153
D	ASP154

site_id	EC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 406

Chain	Residue
D	PRO20
D	GLY57
D	GXP408
D	GXS409
D	HOH524

site_id	EC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO D 407

Chain	Residue
D	PHE147
D	ALA149
D	ILE177
D	ASP178
D	TYR203
D	HOH525

site_id	EC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE GXP D 408

Chain	Residue
D	PRO20
D	PHE52
D	GLY55
D	SER56
D	GLY57
D	TYR145
D	PHE147
D	LYS174
D	THR176
D	GLY202
D	ILE219
D	MG406
D	HOH537

site_id	EC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GXS D 409

Chain	Residue
D	PRO20
D	PHE52
D	GLY55
D	SER56
D	GLY57
D	TYR145
D	PHE147
D	LYS174
D	THR176
D	GLY202
D	MG406
D	HOH537

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	GLY50-GLU67

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

Chain	Residue	Details
A	TYR145-THR176

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Active site: {"description":"Charge relay system","evidences":[{"source":"PubMed","id":"21294156","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Active site: {"description":"Proton donor","evidences":[{"source":"PubMed","id":"21294156","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Active site: {"description":"Schiff-base intermediate with substrate","evidences":[{"source":"PubMed","id":"21294156","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

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