3DU0

E. coli dihydrodipicolinate synthase with first substrate, pyruvate, bound in active site

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	0042802	molecular_function	identical protein binding
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	0042802	molecular_function	identical protein binding
B	0044281	biological_process	small molecule metabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE K A 293

Chain	Residue
A	ALA152
A	VAL154
A	LYS155
A	ILE157

---

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K A 294

Chain	Residue
A	SER48
A	ALA49
A	LEU51
A	GOL296
A	HOH382

---

site_id	AC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GOL A 295

Chain	Residue
A	SER48
A	ALA49
A	GLY78
A	VAL103
A	TYR106
A	GOL296
A	HOH327
A	HOH333
A	HOH382
B	ASN80
B	TYR107

---

site_id	AC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL A 296

Chain	Residue
A	ALA49
A	ASN80
A	TYR106
A	K294
A	GOL295
A	HOH383
B	ASN80
B	TYR106
B	K294
B	GOL295

---

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL A 297

Chain	Residue
A	VAL135
A	PRO136
A	SER137
A	ALA163

---

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL A 298

Chain	Residue
A	GLY165
A	ASN166
A	LEU167
A	HOH318

---

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE K B 293

Chain	Residue
B	ALA152
B	VAL154
B	LYS155
B	ILE157
B	HOH469

---

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE K B 294

Chain	Residue
A	GOL296
A	HOH383
A	HOH384
B	SER48
B	ALA49
B	LEU51
B	HOH412

---

site_id	AC9
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GOL B 295

Chain	Residue
A	ASN80
A	TYR107
A	GOL296
B	SER48
B	ALA49
B	GLY78
B	VAL103
B	TYR106
B	HOH336
B	HOH412
B	HOH434

---

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL B 296

Chain	Residue
B	ASN166
B	LEU167
B	HOH304

---

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL B 297

Chain	Residue
B	PRO136
B	SER137
B	ALA163

---

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ALA38-GLU55

---

site_id	PS00666
Number of Residues	31
Details	DHDPS_2 Dihydrodipicolinate synthase signature 2. YNVPsrTgcdLlpetvgrlakvkn.IiGIKEA

Chain	Residue	Details
A	TYR133-ALA163

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	ACT_SITE: Proton donor/acceptor

Chain	Residue	Details
A	TYR133
B	TYR133

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	ACT_SITE: Schiff-base intermediate with substrate

Chain	Residue	Details
A	KPI161
B	KPI161

---

site_id	SWS_FT_FI3
Number of Residues	4
Details	BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00418, ECO:0000269|PubMed:20353808, ECO:0000269|PubMed:22552955

Chain	Residue	Details
A	THR45
A	ILE203
B	THR45
B	ILE203

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	SITE: Part of a proton relay during catalysis

Chain	Residue	Details
A	THR44
A	TYR107
B	THR44
B	TYR107

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	SITE: L-lysine inhibitor binding; via carbonyl oxygen

Chain	Residue	Details
A	ALA49
B	ALA49

---

site_id	SWS_FT_FI6
Number of Residues	6
Details	SITE: L-lysine inhibitor binding

Chain	Residue	Details
A	ASN80
A	GLU84
A	TYR106
B	ASN80
B	GLU84
B	TYR106

---

Catalytic Information from CSA

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

Chain	Residue	Details
A	ARG138
A	TYR133

---

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

Chain	Residue	Details
B	ARG138
B	TYR133

---

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

Chain	Residue	Details
A	THR44
A	THR45

---

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

Chain	Residue	Details
B	THR44
B	THR45

---

site_id	MCSA1
Number of Residues	6
Details	M-CSA 267

Chain	Residue	Details
A	THR44	hydrogen bond acceptor, hydrogen bond donor
A	TYR107	hydrogen bond donor
A	TYR133	activator, electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
A	ARG138	electrostatic stabiliser
A	KPI161	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
A	ILE203	activator, increase electrophilicity, polar interaction, steric role

---

site_id	MCSA2
Number of Residues	6
Details	M-CSA 267

Chain	Residue	Details
B	THR44	hydrogen bond acceptor, hydrogen bond donor
B	TYR107	hydrogen bond donor
B	TYR133	activator, electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
B	ARG138	electrostatic stabiliser
B	KPI161	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
B	ILE203	activator, increase electrophilicity, polar interaction, steric role

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