Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4L27

Crystal structure of delta1-39 and delta516-525 human cystathionine beta-synthase D444N mutant containing C-terminal 6xHis tag

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0001958	biological_process	endochondral ossification
A	0001974	biological_process	blood vessel remodeling
A	0004122	molecular_function	cystathionine beta-synthase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006534	biological_process	cysteine metabolic process
A	0006535	biological_process	cysteine biosynthetic process from serine
A	0006563	biological_process	L-serine metabolic process
A	0006565	biological_process	L-serine catabolic process
A	0006801	biological_process	superoxide metabolic process
A	0009069	biological_process	serine family amino acid metabolic process
A	0010749	biological_process	regulation of nitric oxide mediated signal transduction
A	0016829	molecular_function	lyase activity
A	0019343	biological_process	cysteine biosynthetic process via cystathionine
A	0019344	biological_process	cysteine biosynthetic process
A	0019346	biological_process	transsulfuration
A	0019448	biological_process	L-cysteine catabolic process
A	0019825	molecular_function	oxygen binding
A	0019899	molecular_function	enzyme binding
A	0020037	molecular_function	heme binding
A	0021587	biological_process	cerebellum morphogenesis
A	0030170	molecular_function	pyridoxal phosphate binding
A	0031625	molecular_function	ubiquitin protein ligase binding
A	0031667	biological_process	response to nutrient levels
A	0042262	biological_process	DNA protection
A	0042802	molecular_function	identical protein binding
A	0042803	molecular_function	protein homodimerization activity
A	0043066	biological_process	negative regulation of apoptotic process
A	0043418	biological_process	homocysteine catabolic process
A	0044272	biological_process	sulfur compound biosynthetic process
A	0046872	molecular_function	metal ion binding
A	0050421	molecular_function	nitrite reductase (NO-forming) activity
A	0050667	biological_process	homocysteine metabolic process
A	0051593	biological_process	response to folic acid
A	0060135	biological_process	maternal process involved in female pregnancy
A	0060351	biological_process	cartilage development involved in endochondral bone morphogenesis
A	0070025	molecular_function	carbon monoxide binding
A	0070026	molecular_function	nitric oxide binding
A	0070814	biological_process	hydrogen sulfide biosynthetic process
A	0071456	biological_process	cellular response to hypoxia
A	0072341	molecular_function	modified amino acid binding
A	0097746	biological_process	blood vessel diameter maintenance
A	1904047	molecular_function	S-adenosyl-L-methionine binding
B	0001958	biological_process	endochondral ossification
B	0001974	biological_process	blood vessel remodeling
B	0004122	molecular_function	cystathionine beta-synthase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006534	biological_process	cysteine metabolic process
B	0006535	biological_process	cysteine biosynthetic process from serine
B	0006563	biological_process	L-serine metabolic process
B	0006565	biological_process	L-serine catabolic process
B	0006801	biological_process	superoxide metabolic process
B	0009069	biological_process	serine family amino acid metabolic process
B	0010749	biological_process	regulation of nitric oxide mediated signal transduction
B	0016829	molecular_function	lyase activity
B	0019343	biological_process	cysteine biosynthetic process via cystathionine
B	0019344	biological_process	cysteine biosynthetic process
B	0019346	biological_process	transsulfuration
B	0019448	biological_process	L-cysteine catabolic process
B	0019825	molecular_function	oxygen binding
B	0019899	molecular_function	enzyme binding
B	0020037	molecular_function	heme binding
B	0021587	biological_process	cerebellum morphogenesis
B	0030170	molecular_function	pyridoxal phosphate binding
B	0031625	molecular_function	ubiquitin protein ligase binding
B	0031667	biological_process	response to nutrient levels
B	0042262	biological_process	DNA protection
B	0042802	molecular_function	identical protein binding
B	0042803	molecular_function	protein homodimerization activity
B	0043066	biological_process	negative regulation of apoptotic process
B	0043418	biological_process	homocysteine catabolic process
B	0044272	biological_process	sulfur compound biosynthetic process
B	0046872	molecular_function	metal ion binding
B	0050421	molecular_function	nitrite reductase (NO-forming) activity
B	0050667	biological_process	homocysteine metabolic process
B	0051593	biological_process	response to folic acid
B	0060135	biological_process	maternal process involved in female pregnancy
B	0060351	biological_process	cartilage development involved in endochondral bone morphogenesis
B	0070025	molecular_function	carbon monoxide binding
B	0070026	molecular_function	nitric oxide binding
B	0070814	biological_process	hydrogen sulfide biosynthetic process
B	0071456	biological_process	cellular response to hypoxia
B	0072341	molecular_function	modified amino acid binding
B	0097746	biological_process	blood vessel diameter maintenance
B	1904047	molecular_function	S-adenosyl-L-methionine binding
C	0001958	biological_process	endochondral ossification
C	0001974	biological_process	blood vessel remodeling
C	0004122	molecular_function	cystathionine beta-synthase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006534	biological_process	cysteine metabolic process
C	0006535	biological_process	cysteine biosynthetic process from serine
C	0006563	biological_process	L-serine metabolic process
C	0006565	biological_process	L-serine catabolic process
C	0006801	biological_process	superoxide metabolic process
C	0009069	biological_process	serine family amino acid metabolic process
C	0010749	biological_process	regulation of nitric oxide mediated signal transduction
C	0016829	molecular_function	lyase activity
C	0019343	biological_process	cysteine biosynthetic process via cystathionine
C	0019344	biological_process	cysteine biosynthetic process
C	0019346	biological_process	transsulfuration
C	0019448	biological_process	L-cysteine catabolic process
C	0019825	molecular_function	oxygen binding
C	0019899	molecular_function	enzyme binding
C	0020037	molecular_function	heme binding
C	0021587	biological_process	cerebellum morphogenesis
C	0030170	molecular_function	pyridoxal phosphate binding
C	0031625	molecular_function	ubiquitin protein ligase binding
C	0031667	biological_process	response to nutrient levels
C	0042262	biological_process	DNA protection
C	0042802	molecular_function	identical protein binding
C	0042803	molecular_function	protein homodimerization activity
C	0043066	biological_process	negative regulation of apoptotic process
C	0043418	biological_process	homocysteine catabolic process
C	0044272	biological_process	sulfur compound biosynthetic process
C	0046872	molecular_function	metal ion binding
C	0050421	molecular_function	nitrite reductase (NO-forming) activity
C	0050667	biological_process	homocysteine metabolic process
C	0051593	biological_process	response to folic acid
C	0060135	biological_process	maternal process involved in female pregnancy
C	0060351	biological_process	cartilage development involved in endochondral bone morphogenesis
C	0070025	molecular_function	carbon monoxide binding
C	0070026	molecular_function	nitric oxide binding
C	0070814	biological_process	hydrogen sulfide biosynthetic process
C	0071456	biological_process	cellular response to hypoxia
C	0072341	molecular_function	modified amino acid binding
C	0097746	biological_process	blood vessel diameter maintenance
C	1904047	molecular_function	S-adenosyl-L-methionine binding
D	0001958	biological_process	endochondral ossification
D	0001974	biological_process	blood vessel remodeling
D	0004122	molecular_function	cystathionine beta-synthase activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006534	biological_process	cysteine metabolic process
D	0006535	biological_process	cysteine biosynthetic process from serine
D	0006563	biological_process	L-serine metabolic process
D	0006565	biological_process	L-serine catabolic process
D	0006801	biological_process	superoxide metabolic process
D	0009069	biological_process	serine family amino acid metabolic process
D	0010749	biological_process	regulation of nitric oxide mediated signal transduction
D	0016829	molecular_function	lyase activity
D	0019343	biological_process	cysteine biosynthetic process via cystathionine
D	0019344	biological_process	cysteine biosynthetic process
D	0019346	biological_process	transsulfuration
D	0019448	biological_process	L-cysteine catabolic process
D	0019825	molecular_function	oxygen binding
D	0019899	molecular_function	enzyme binding
D	0020037	molecular_function	heme binding
D	0021587	biological_process	cerebellum morphogenesis
D	0030170	molecular_function	pyridoxal phosphate binding
D	0031625	molecular_function	ubiquitin protein ligase binding
D	0031667	biological_process	response to nutrient levels
D	0042262	biological_process	DNA protection
D	0042802	molecular_function	identical protein binding
D	0042803	molecular_function	protein homodimerization activity
D	0043066	biological_process	negative regulation of apoptotic process
D	0043418	biological_process	homocysteine catabolic process
D	0044272	biological_process	sulfur compound biosynthetic process
D	0046872	molecular_function	metal ion binding
D	0050421	molecular_function	nitrite reductase (NO-forming) activity
D	0050667	biological_process	homocysteine metabolic process
D	0051593	biological_process	response to folic acid
D	0060135	biological_process	maternal process involved in female pregnancy
D	0060351	biological_process	cartilage development involved in endochondral bone morphogenesis
D	0070025	molecular_function	carbon monoxide binding
D	0070026	molecular_function	nitric oxide binding
D	0070814	biological_process	hydrogen sulfide biosynthetic process
D	0071456	biological_process	cellular response to hypoxia
D	0072341	molecular_function	modified amino acid binding
D	0097746	biological_process	blood vessel diameter maintenance
D	1904047	molecular_function	S-adenosyl-L-methionine binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	14
Details	BINDING SITE FOR RESIDUE PLP B 601

Chain	Residue
B	LYS119
B	ILE306
B	SER349
B	PRO375
B	ASP376
B	TYR381
B	SER147
B	ASN149
B	VAL255
B	GLY256
B	THR257
B	GLY258
B	GLY259
B	THR260

site_id	AC2
Number of Residues	16
Details	BINDING SITE FOR RESIDUE HEM B 602

Chain	Residue
B	ARG51
B	CYS52
B	THR53
B	TRP54
B	ARG58
B	GLU62
B	SER63
B	PRO64
B	HIS65
B	ARG224
B	ALA226
B	PRO229
B	LEU230
B	TYR233
B	ARG266
B	VAL314

site_id	AC3
Number of Residues	15
Details	BINDING SITE FOR RESIDUE PLP D 601

Chain	Residue
D	LYS119
D	ASN149
D	SER254
D	VAL255
D	GLY256
D	THR257
D	GLY258
D	GLY259
D	THR260
D	GLY305
D	ILE306
D	SER349
D	PRO375
D	ASP376
D	TYR381

site_id	AC4
Number of Residues	18
Details	BINDING SITE FOR RESIDUE HEM D 602

Chain	Residue
D	PRO49
D	SER50
D	ARG51
D	CYS52
D	THR53
D	TRP54
D	ARG58
D	PRO59
D	GLU62
D	SER63
D	PRO64
D	HIS65
D	ARG224
D	ALA226
D	PRO229
D	TYR233
D	ARG266
D	THR313

site_id	AC5
Number of Residues	15
Details	BINDING SITE FOR RESIDUE PLP A 601

Chain	Residue
A	LYS119
A	ASN149
A	SER254
A	VAL255
A	GLY256
A	THR257
A	GLY258
A	GLY259
A	THR260
A	GLU304
A	ILE306
A	SER349
A	PRO375
A	ASP376
A	TYR381

site_id	AC6
Number of Residues	17
Details	BINDING SITE FOR RESIDUE HEM A 602

Chain	Residue
A	SER50
A	ARG51
A	CYS52
A	THR53
A	TRP54
A	ARG58
A	SER63
A	PRO64
A	HIS65
A	ALA226
A	PRO229
A	THR262
A	GLY263
A	ARG266
A	THR313
A	VAL314
D	ARG51

site_id	AC7
Number of Residues	13
Details	BINDING SITE FOR RESIDUE PLP C 601

Chain	Residue
C	THR257
C	GLY258
C	GLY259
C	THR260
C	ILE306
C	SER349
C	PRO375
C	ASP376
C	TYR381
C	LYS119
C	ASN149
C	VAL255
C	GLY256

site_id	AC8
Number of Residues	16
Details	BINDING SITE FOR RESIDUE HEM C 602

Chain	Residue
C	PRO49
C	SER50
C	ARG51
C	CYS52
C	THR53
C	TRP54
C	SER63
C	PRO64
C	HIS65
C	ARG224
C	ALA226
C	PRO229
C	TYR233
C	GLY263
C	ARG266
C	VAL314

Functional Information from PROSITE/UniProt

site_id	PS00901
Number of Residues	19
Details	CYS_SYNTHASE Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. KcEffn.AGgSVKdRiSlrM

Chain	Residue	Details
B	LYS108-MET126

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	BINDING: axial binding residue => ECO:0000269\|PubMed:11483494, ECO:0000269\|PubMed:12173932

Chain	Residue	Details
B	CYS52
B	HIS65
D	CYS52
D	HIS65
A	CYS52
A	HIS65
C	CYS52
C	HIS65

site_id	SWS_FT_FI2
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269\|PubMed:11483494, ECO:0000269\|PubMed:12173932

Chain	Residue	Details
B	ASN149
C	ASN149
C	GLY256
C	SER349
B	GLY256
B	SER349
D	ASN149
D	GLY256
D	SER349
A	ASN149
A	GLY256
A	SER349

site_id	SWS_FT_FI3
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:21406692

Chain	Residue	Details
B	SER27
D	SER27
A	SER27
C	SER27

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000269\|PubMed:11483494, ECO:0000269\|PubMed:12173932

Chain	Residue	Details
B	LYS119
D	LYS119
A	LYS119
C	LYS119

site_id	SWS_FT_FI5
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
B	SER199
D	SER199
A	SER199
C	SER199

site_id	SWS_FT_FI6
Number of Residues	8
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) => ECO:0000269\|PubMed:17087506

Chain	Residue	Details
B	LYS211
D	LYS211
A	LYS211
C	LYS211

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	1
Details	M-CSA 713

Chain	Residue	Details
B	LYS119	covalently attached, electron pair acceptor, electron pair donor, nucleofuge, nucleophile, proton acceptor, proton donor, proton relay

site_id	MCSA2
Number of Residues	1
Details	M-CSA 713

Chain	Residue	Details
D	LYS119	covalently attached, electron pair acceptor, electron pair donor, nucleofuge, nucleophile, proton acceptor, proton donor, proton relay

site_id	MCSA3
Number of Residues	1
Details	M-CSA 713

Chain	Residue	Details
A	LYS119	covalently attached, electron pair acceptor, electron pair donor, nucleofuge, nucleophile, proton acceptor, proton donor, proton relay

site_id	MCSA4
Number of Residues	1
Details	M-CSA 713

Chain	Residue	Details
C	LYS119	covalently attached, electron pair acceptor, electron pair donor, nucleofuge, nucleophile, proton acceptor, proton donor, proton relay

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