Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6C4C

Crystal structure of 3-nitropropionate modified isocitrate lyase from Mycobacterium tuberculosis with glyoxylate and pyruvate

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
E	0003824	molecular_function	catalytic activity
E	0004451	molecular_function	isocitrate lyase activity
E	0005576	cellular_component	extracellular region
E	0005829	cellular_component	cytosol
E	0005886	cellular_component	plasma membrane
E	0006097	biological_process	glyoxylate cycle
E	0006099	biological_process	tricarboxylic acid cycle
E	0006102	biological_process	isocitrate metabolic process
E	0016829	molecular_function	lyase activity
E	0019752	biological_process	carboxylic acid metabolic process
E	0035375	molecular_function	zymogen binding
E	0046421	molecular_function	methylisocitrate lyase activity
E	0046872	molecular_function	metal ion binding
E	0052572	biological_process	response to host immune response
E	0071456	biological_process	cellular response to hypoxia
F	0003824	molecular_function	catalytic activity
F	0004451	molecular_function	isocitrate lyase activity
F	0005576	cellular_component	extracellular region
F	0005829	cellular_component	cytosol
F	0005886	cellular_component	plasma membrane
F	0006097	biological_process	glyoxylate cycle
F	0006099	biological_process	tricarboxylic acid cycle
F	0006102	biological_process	isocitrate metabolic process
F	0016829	molecular_function	lyase activity
F	0019752	biological_process	carboxylic acid metabolic process
F	0035375	molecular_function	zymogen binding
F	0046421	molecular_function	methylisocitrate lyase activity
F	0046872	molecular_function	metal ion binding
F	0052572	biological_process	response to host immune response
F	0071456	biological_process	cellular response to hypoxia
G	0003824	molecular_function	catalytic activity
G	0004451	molecular_function	isocitrate lyase activity
G	0005576	cellular_component	extracellular region
G	0005829	cellular_component	cytosol
G	0005886	cellular_component	plasma membrane
G	0006097	biological_process	glyoxylate cycle
G	0006099	biological_process	tricarboxylic acid cycle
G	0006102	biological_process	isocitrate metabolic process
G	0016829	molecular_function	lyase activity
G	0019752	biological_process	carboxylic acid metabolic process
G	0035375	molecular_function	zymogen binding
G	0046421	molecular_function	methylisocitrate lyase activity
G	0046872	molecular_function	metal ion binding
G	0052572	biological_process	response to host immune response
G	0071456	biological_process	cellular response to hypoxia
H	0003824	molecular_function	catalytic activity
H	0004451	molecular_function	isocitrate lyase activity
H	0005576	cellular_component	extracellular region
H	0005829	cellular_component	cytosol
H	0005886	cellular_component	plasma membrane
H	0006097	biological_process	glyoxylate cycle
H	0006099	biological_process	tricarboxylic acid cycle
H	0006102	biological_process	isocitrate metabolic process
H	0016829	molecular_function	lyase activity
H	0019752	biological_process	carboxylic acid metabolic process
H	0035375	molecular_function	zymogen binding
H	0046421	molecular_function	methylisocitrate lyase activity
H	0046872	molecular_function	metal ion binding
H	0052572	biological_process	response to host immune response
H	0071456	biological_process	cellular response to hypoxia

Functional Information from PDB Data

site_id	AC1
Number of Residues	11
Details	binding site for residue GLV A 501

Chain	Residue
A	TYR89
A	THR347
A	MG502
A	SER91
A	GLY92
A	TRP93
A	ASP153
A	HIS180
A	EJA191
A	ARG228
A	TRP283

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

Chain	Residue
A	ASP108
A	ASP153
A	GLV501
A	HOH603
A	HOH610
A	HOH653

site_id	AC3
Number of Residues	6
Details	binding site for residue MG A 503

Chain	Residue
A	ALA276
A	ALA279
A	GLN308
A	HOH666
A	HOH797
A	HOH816

site_id	AC4
Number of Residues	15
Details	binding site for residue PYR B 501

Chain	Residue
B	TYR89
B	SER91
B	GLY92
B	TRP93
B	ASP108
B	ASP153
B	HIS180
B	EJA191
B	ARG228
B	TRP283
B	THR347
B	MG502
B	HOH604
B	HOH613
B	HOH661

site_id	AC5
Number of Residues	6
Details	binding site for residue MG B 502

Chain	Residue
B	ASP108
B	ASP153
B	PYR501
B	HOH604
B	HOH613
B	HOH661

site_id	AC6
Number of Residues	6
Details	binding site for residue MG B 503

Chain	Residue
B	ALA276
B	ALA279
B	GLN308
B	HOH659
B	HOH771
B	HOH773

site_id	AC7
Number of Residues	14
Details	binding site for residue PYR C 501

Chain	Residue
C	TYR89
C	SER91
C	GLY92
C	TRP93
C	ASP153
C	HIS180
C	EJA191
C	ARG228
C	TRP283
C	THR347
C	MG502
C	HOH604
C	HOH619
C	HOH636

site_id	AC8
Number of Residues	5
Details	binding site for residue MG C 502

Chain	Residue
C	ASP153
C	PYR501
C	HOH604
C	HOH619
C	HOH636

site_id	AC9
Number of Residues	6
Details	binding site for residue MG C 503

Chain	Residue
C	ALA276
C	ALA279
C	GLN308
C	HOH637
C	HOH766
C	HOH770

site_id	AD1
Number of Residues	12
Details	binding site for residue GLV D 501

Chain	Residue
D	TYR89
D	SER91
D	GLY92
D	TRP93
D	ASP153
D	HIS180
D	EJA191
D	ARG228
D	THR347
D	MG502
D	HOH601
D	HOH628

site_id	AD2
Number of Residues	6
Details	binding site for residue MG D 502

Chain	Residue
D	ASP108
D	ASP153
D	GLV501
D	HOH601
D	HOH628
D	HOH641

site_id	AD3
Number of Residues	6
Details	binding site for residue MG D 503

Chain	Residue
D	ALA276
D	ALA279
D	GLN308
D	HOH617
D	HOH765
D	HOH769

site_id	AD4
Number of Residues	14
Details	binding site for residue PYR E 501

Chain	Residue
E	TYR89
E	SER91
E	GLY92
E	TRP93
E	ASP108
E	ASP153
E	EJA191
E	ARG228
E	TRP283
E	THR347
E	MG502
E	HOH604
E	HOH612
E	HOH658

site_id	AD5
Number of Residues	6
Details	binding site for residue MG E 502

Chain	Residue
E	ASP108
E	ASP153
E	PYR501
E	HOH604
E	HOH612
E	HOH658

site_id	AD6
Number of Residues	6
Details	binding site for residue MG E 503

Chain	Residue
E	ALA276
E	ALA279
E	GLN308
E	HOH602
E	HOH769
E	HOH788

site_id	AD7
Number of Residues	10
Details	binding site for residue 3NP E 504

Chain	Residue
E	TYR356
E	SER357
E	LEU376
E	ARG379
E	HOH601
E	HOH605
E	HOH757
F	TYR356
F	SER357
F	ARG379

site_id	AD8
Number of Residues	12
Details	binding site for residue PYR F 501

Chain	Residue
F	TYR89
F	SER91
F	GLY92
F	TRP93
F	ASP153
F	EJA191
F	ARG228
F	TRP283
F	THR347
F	MG502
F	HOH608
F	HOH661

site_id	AD9
Number of Residues	6
Details	binding site for residue MG F 502

Chain	Residue
F	ASP108
F	ASP153
F	PYR501
F	HOH608
F	HOH617
F	HOH661

site_id	AE1
Number of Residues	14
Details	binding site for residue PYR G 501

Chain	Residue
G	TYR89
G	SER91
G	GLY92
G	TRP93
G	ASP108
G	ASP153
G	EJA191
G	ARG228
G	TRP283
G	THR347
G	MG502
G	HOH606
G	HOH614
G	HOH650

site_id	AE2
Number of Residues	6
Details	binding site for residue MG G 502

Chain	Residue
G	ASP108
G	ASP153
G	PYR501
G	HOH606
G	HOH614
G	HOH650

site_id	AE3
Number of Residues	5
Details	binding site for residue MG G 503

Chain	Residue
G	ALA276
G	ALA279
G	GLN308
G	HOH736
G	HOH771

site_id	AE4
Number of Residues	5
Details	binding site for residue MG H 501

Chain	Residue
E	HOH768
H	ASP34
H	HOH657
H	HOH683
H	HOH746

site_id	AE5
Number of Residues	14
Details	binding site for residue GLV H 502

Chain	Residue
H	TYR89
H	SER91
H	GLY92
H	TRP93
H	ASP108
H	ASP153
H	HIS180
H	EJA191
H	ARG228
H	THR347
H	MG503
H	HOH601
H	HOH606
H	HOH621

site_id	AE6
Number of Residues	6
Details	binding site for residue MG H 503

Chain	Residue
H	ASP108
H	ASP153
H	GLV502
H	HOH601
H	HOH606
H	HOH621

site_id	AE7
Number of Residues	6
Details	binding site for residue MG H 504

Chain	Residue
H	ALA276
H	ALA279
H	GLN308
H	HOH679
H	HOH761
H	HOH767

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	ACT_SITE: Proton acceptor => ECO:0000305\|PubMed:24354272

Chain	Residue	Details
A	EJA191
B	EJA191
C	EJA191
D	EJA191
E	EJA191
F	EJA191
G	EJA191
H	EJA191

site_id	SWS_FT_FI2
Number of Residues	48
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
E	SER91
E	ASP153
E	GLY192
E	ARG228
E	ASN313
A	GLY192
E	THR347
F	SER91
F	ASP153
F	GLY192
F	ARG228
F	ASN313
F	THR347
G	SER91
G	ASP153
G	GLY192
A	ARG228
G	ARG228
G	ASN313
G	THR347
H	SER91
H	ASP153
H	GLY192
H	ARG228
H	ASN313
H	THR347
A	ASN313
A	THR347
B	SER91
B	ASP153
B	GLY192

site_id	SWS_FT_FI3
Number of Residues	16
Details	CROSSLNK: Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-Cter in protein Pup) => ECO:0000269\|PubMed:20066036

Chain	Residue	Details
A	LYS334
F	LYS334
G	LYS334
H	LYS334
B	LYS334
C	LYS334
D	LYS334
E	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	EJA191	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	EJA191	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	EJA191	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	EJA191	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

site_id	MCSA5
Number of Residues	7
Details	M-CSA 272

Chain	Residue	Details
E	ASP153	metal ligand
E	HIS180	electrostatic stabiliser, hydrogen bond donor
E	EJA191	covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
E	HIS193	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
E	ARG228	electrostatic stabiliser, hydrogen bond donor
E	SER315	electrostatic stabiliser, hydrogen bond donor
E	SER317	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA6
Number of Residues	7
Details	M-CSA 272

Chain	Residue	Details
F	ASP153	metal ligand
F	HIS180	electrostatic stabiliser, hydrogen bond donor
F	EJA191	covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
F	HIS193	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
F	ARG228	electrostatic stabiliser, hydrogen bond donor
F	SER315	electrostatic stabiliser, hydrogen bond donor
F	SER317	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA7
Number of Residues	7
Details	M-CSA 272

Chain	Residue	Details
G	ASP153	metal ligand
G	HIS180	electrostatic stabiliser, hydrogen bond donor
G	EJA191	covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
G	HIS193	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
G	ARG228	electrostatic stabiliser, hydrogen bond donor
G	SER315	electrostatic stabiliser, hydrogen bond donor
G	SER317	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA8
Number of Residues	7
Details	M-CSA 272

Chain	Residue	Details
H	ASP153	metal ligand
H	HIS180	electrostatic stabiliser, hydrogen bond donor
H	EJA191	covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base)
H	HIS193	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base)
H	ARG228	electrostatic stabiliser, hydrogen bond donor
H	SER315	electrostatic stabiliser, hydrogen bond donor
H	SER317	electrostatic stabiliser, hydrogen bond donor

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