Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5DQL

Crystal Structure of 2-vinyl glyoxylate modified isocitrate lyase from Mycobacterium tuberculosis

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0004451	molecular_function	isocitrate lyase activity
A	0005576	cellular_component	extracellular region
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0006097	biological_process	glyoxylate cycle
A	0006099	biological_process	tricarboxylic acid cycle
A	0006102	biological_process	isocitrate metabolic process
A	0016829	molecular_function	lyase activity
A	0019752	biological_process	carboxylic acid metabolic process
A	0035375	molecular_function	zymogen binding
A	0046421	molecular_function	methylisocitrate lyase activity
A	0046872	molecular_function	metal ion binding
A	0052572	biological_process	response to host immune response
A	0071456	biological_process	cellular response to hypoxia
B	0003824	molecular_function	catalytic activity
B	0004451	molecular_function	isocitrate lyase activity
B	0005576	cellular_component	extracellular region
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
B	0006097	biological_process	glyoxylate cycle
B	0006099	biological_process	tricarboxylic acid cycle
B	0006102	biological_process	isocitrate metabolic process
B	0016829	molecular_function	lyase activity
B	0019752	biological_process	carboxylic acid metabolic process
B	0035375	molecular_function	zymogen binding
B	0046421	molecular_function	methylisocitrate lyase activity
B	0046872	molecular_function	metal ion binding
B	0052572	biological_process	response to host immune response
B	0071456	biological_process	cellular response to hypoxia
C	0003824	molecular_function	catalytic activity
C	0004451	molecular_function	isocitrate lyase activity
C	0005576	cellular_component	extracellular region
C	0005829	cellular_component	cytosol
C	0005886	cellular_component	plasma membrane
C	0006097	biological_process	glyoxylate cycle
C	0006099	biological_process	tricarboxylic acid cycle
C	0006102	biological_process	isocitrate metabolic process
C	0016829	molecular_function	lyase activity
C	0019752	biological_process	carboxylic acid metabolic process
C	0035375	molecular_function	zymogen binding
C	0046421	molecular_function	methylisocitrate lyase activity
C	0046872	molecular_function	metal ion binding
C	0052572	biological_process	response to host immune response
C	0071456	biological_process	cellular response to hypoxia
D	0003824	molecular_function	catalytic activity
D	0004451	molecular_function	isocitrate lyase activity
D	0005576	cellular_component	extracellular region
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
D	0006097	biological_process	glyoxylate cycle
D	0006099	biological_process	tricarboxylic acid cycle
D	0006102	biological_process	isocitrate metabolic process
D	0016829	molecular_function	lyase activity
D	0019752	biological_process	carboxylic acid metabolic process
D	0035375	molecular_function	zymogen binding
D	0046421	molecular_function	methylisocitrate lyase activity
D	0046872	molecular_function	metal ion binding
D	0052572	biological_process	response to host immune response
D	0071456	biological_process	cellular response to hypoxia

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue MG A 501

Chain	Residue
A	ASP153
A	HOH604
A	HOH647
A	HOH787
A	HOH879

site_id	AC2
Number of Residues	6
Details	binding site for residue MG A 502

Chain	Residue
A	HOH669
A	HOH869
A	ALA276
A	ALA279
A	GLN308
A	HOH666

site_id	AC3
Number of Residues	12
Details	binding site for residue VGX A 503

Chain	Residue
A	TRP93
A	ASP108
A	CYS191
A	GLY192
A	HIS193
A	ASN313
A	SER315
A	SER317
A	THR347
A	LEU348
A	HOH603
A	HOH787

site_id	AC4
Number of Residues	7
Details	binding site for residue MG B 501

Chain	Residue
B	ASP108
B	ASP153
B	HOH637
B	HOH674
B	HOH694
B	HOH699
B	HOH855

site_id	AC5
Number of Residues	7
Details	binding site for residue MG C 501

Chain	Residue
C	ASP108
C	ASP153
C	HOH616
C	HOH696
C	HOH698
C	HOH766
C	HOH821

site_id	AC6
Number of Residues	8
Details	binding site for residue MG D 501

Chain	Residue
D	TRP93
D	ASP108
D	ASP153
D	HOH602
D	HOH659
D	HOH666
D	HOH724
D	HOH818

site_id	AC7
Number of Residues	14
Details	binding site for Di-peptide VGX B 502 and CYS B 191

Chain	Residue
A	GLN394
B	TRP93
B	ASP108
B	LYS190
B	GLY192
B	HIS193
B	LEU194
B	ASN313
B	SER315
B	SER317
B	THR347
B	LEU348
B	HOH641
B	HOH694

site_id	AC8
Number of Residues	13
Details	binding site for Di-peptide VGX C 502 and CYS C 191

Chain	Residue
C	TRP93
C	ASP108
C	LYS190
C	GLY192
C	HIS193
C	LEU194
C	ASN313
C	SER315
C	SER317
C	THR347
C	LEU348
C	HOH605
D	GLN394

site_id	AC9
Number of Residues	11
Details	binding site for Di-peptide VGX D 502 and CYS D 191

Chain	Residue
C	GLN394
D	TRP93
D	ASP108
D	LYS190
D	GLY192
D	HIS193
D	LEU194
D	ASN313
D	SER315
D	SER317
D	THR347

Functional Information from PROSITE/UniProt

site_id	PS00161
Number of Residues	6
Details	ISOCITRATE_LYASE Isocitrate lyase signature. KKCGHL

Chain	Residue	Details
A	LYS189-LEU194

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE: Proton acceptor => ECO:0000305\|PubMed:24354272

Chain	Residue	Details
A	CYS191
B	CYS191
C	CYS191
D	CYS191

site_id	SWS_FT_FI2
Number of Residues	24
Details	BINDING: BINDING => ECO:0000269\|PubMed:10932251

Chain	Residue	Details
A	SER91
B	ARG228
B	ASN313
B	THR347
C	SER91
C	ASP153
C	GLY192
C	ARG228
C	ASN313
C	THR347
D	SER91
A	ASP153
D	ASP153
D	GLY192
D	ARG228
D	ASN313
D	THR347
A	GLY192
A	ARG228
A	ASN313
A	THR347
B	SER91
B	ASP153
B	GLY192

site_id	SWS_FT_FI3
Number of Residues	8
Details	CROSSLNK: Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-Cter in protein Pup) => ECO:0000269\|PubMed:20066036

Chain	Residue	Details
A	LYS334
B	LYS334
C	LYS334
D	LYS334

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	7
Details	M-CSA 272

Chain	Residue	Details
A	ASP153	metal ligand
A	HIS180	electrostatic stabiliser, hydrogen bond donor
A	CYS191	covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
A	HIS193	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
A	ARG228	electrostatic stabiliser, hydrogen bond donor
A	SER315	electrostatic stabiliser, hydrogen bond donor
A	SER317	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA2
Number of Residues	7
Details	M-CSA 272

Chain	Residue	Details
B	ASP153	metal ligand
B	HIS180	electrostatic stabiliser, hydrogen bond donor
B	CYS191	covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
B	HIS193	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
B	ARG228	electrostatic stabiliser, hydrogen bond donor
B	SER315	electrostatic stabiliser, hydrogen bond donor
B	SER317	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA3
Number of Residues	7
Details	M-CSA 272

Chain	Residue	Details
C	ASP153	metal ligand
C	HIS180	electrostatic stabiliser, hydrogen bond donor
C	CYS191	covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
C	HIS193	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
C	ARG228	electrostatic stabiliser, hydrogen bond donor
C	SER315	electrostatic stabiliser, hydrogen bond donor
C	SER317	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA4
Number of Residues	7
Details	M-CSA 272

Chain	Residue	Details
D	ASP153	metal ligand
D	HIS180	electrostatic stabiliser, hydrogen bond donor
D	CYS191	covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
D	HIS193	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
D	ARG228	electrostatic stabiliser, hydrogen bond donor
D	SER315	electrostatic stabiliser, hydrogen bond donor
D	SER317	electrostatic stabiliser, hydrogen bond donor

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