Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3T89

Crystal structure of Escherichia coli MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase in vitamin K2 biosynthesis

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0005515	molecular_function	protein binding
A	0005829	cellular_component	cytosol
A	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
A	0009234	biological_process	menaquinone biosynthetic process
A	0016829	molecular_function	lyase activity
A	0071890	molecular_function	bicarbonate binding
B	0003824	molecular_function	catalytic activity
B	0005515	molecular_function	protein binding
B	0005829	cellular_component	cytosol
B	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
B	0009234	biological_process	menaquinone biosynthetic process
B	0016829	molecular_function	lyase activity
B	0071890	molecular_function	bicarbonate binding
C	0003824	molecular_function	catalytic activity
C	0005515	molecular_function	protein binding
C	0005829	cellular_component	cytosol
C	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
C	0009234	biological_process	menaquinone biosynthetic process
C	0016829	molecular_function	lyase activity
C	0071890	molecular_function	bicarbonate binding
D	0003824	molecular_function	catalytic activity
D	0005515	molecular_function	protein binding
D	0005829	cellular_component	cytosol
D	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
D	0009234	biological_process	menaquinone biosynthetic process
D	0016829	molecular_function	lyase activity
D	0071890	molecular_function	bicarbonate binding
E	0003824	molecular_function	catalytic activity
E	0005515	molecular_function	protein binding
E	0005829	cellular_component	cytosol
E	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
E	0009234	biological_process	menaquinone biosynthetic process
E	0016829	molecular_function	lyase activity
E	0071890	molecular_function	bicarbonate binding
F	0003824	molecular_function	catalytic activity
F	0005515	molecular_function	protein binding
F	0005829	cellular_component	cytosol
F	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
F	0009234	biological_process	menaquinone biosynthetic process
F	0016829	molecular_function	lyase activity
F	0071890	molecular_function	bicarbonate binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE MLI A 301

Chain	Residue
A	GLY132
A	HOH314
A	GLY133
A	GLN154
A	THR155
A	GLY156
A	SER161
A	PHE162
A	ASP163
A	TRP184

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 302

Chain	Residue
A	THR203
A	VAL205
A	GLU213
A	ARG216
A	TRP217
A	HOH462
C	ARG188

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL A 303

Chain	Residue
A	ILE174
A	HOH350
D	ILE174

site_id	AC4
Number of Residues	11
Details	BINDING SITE FOR RESIDUE MLI B 301

Chain	Residue
B	GLY132
B	GLY133
B	GLN154
B	THR155
B	GLY156
B	SER161
B	PHE162
B	ASP163
B	TRP184
B	HOH525
B	HOH705

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL B 302

Chain	Residue
B	THR203
B	VAL205
B	GLU213
B	ARG216
B	TRP217
E	ARG188

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL B 304

Chain	Residue
B	PHE22
B	GLU23
B	ILE25
B	ASN40

site_id	AC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE MLI C 301

Chain	Residue
C	GLY132
C	GLY133
C	GLN154
C	THR155
C	GLY156
C	SER161
C	PHE162
C	ASP163
C	TRP184
C	HOH437

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL C 302

Chain	Residue
C	THR203
C	VAL205
C	GLU213
C	ARG216
C	TRP217
D	ARG188

site_id	AC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE MLI D 301

Chain	Residue
D	GLY132
D	GLN154
D	THR155
D	GLY156
D	SER161
D	PHE162
D	ASP163
D	TRP184

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL D 302

Chain	Residue
A	ARG188
D	THR203
D	VAL205
D	GLU213
D	ARG216
D	TRP217

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL E 303

Chain	Residue
E	ALA172
E	VAL175
E	GLY176
E	HOH321
F	ILE174
F	VAL175
F	GLY176

site_id	BC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE MLI E 301

Chain	Residue
E	GLY132
E	GLY133
E	GLN154
E	THR155
E	GLY156
E	SER161
E	PHE162
E	ASP163
E	TRP184

site_id	BC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL E 302

Chain	Residue
E	THR203
E	VAL205
E	GLU213
E	ARG216
E	TRP217
E	HOH343
F	ARG188

site_id	BC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE MLI F 301

Chain	Residue
F	PHE162
F	ASP163
F	TRP184
F	HOH495
F	GLY132
F	GLN154
F	THR155
F	GLY156
F	SER161

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL F 302

Chain	Residue
B	ARG188
F	THR203
F	VAL205
F	GLU213
F	ARG216
F	TRP217

Functional Information from PROSITE/UniProt

site_id	PS00166
Number of Residues	21
Details	ENOYL_COA_HYDRATASE Enoyl-CoA hydratase/isomerase signature. VAmVAGysiGGGhvlhMmCDL

Chain	Residue	Details
A	VAL123-LEU143

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	36
Details	Binding site: {"description":"in other chain","evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21830810","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23658663","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	10
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"21830810","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23658663","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"22606952","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	6
Details	Binding site: {"description":"in other chain","evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"23658663","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21830810","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21830810","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23658663","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	6
Details	Site: {"description":"Important for catalysis","evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21830810","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

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