Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1BU6

CRYSTAL STRUCTURES OF ESCHERICHIA COLI GLYCEROL KINASE AND THE MUTANT A65T IN AN INACTIVE TETRAMER: CONFORMATIONAL CHANGES AND IMPLICATIONS FOR ALLOSTERIC REGULATION

Functional Information from GO Data

Chain	GOid	namespace	contents
O	0000166	molecular_function	nucleotide binding
O	0003824	molecular_function	catalytic activity
O	0004370	molecular_function	glycerol kinase activity
O	0005515	molecular_function	protein binding
O	0005524	molecular_function	ATP binding
O	0005829	cellular_component	cytosol
O	0005975	biological_process	carbohydrate metabolic process
O	0006071	biological_process	glycerol metabolic process
O	0006072	biological_process	glycerol-3-phosphate metabolic process
O	0006974	biological_process	DNA damage response
O	0008270	molecular_function	zinc ion binding
O	0016301	molecular_function	kinase activity
O	0016310	biological_process	phosphorylation
O	0016740	molecular_function	transferase activity
O	0016773	molecular_function	phosphotransferase activity, alcohol group as acceptor
O	0019563	biological_process	glycerol catabolic process
O	0042802	molecular_function	identical protein binding
O	0046872	molecular_function	metal ion binding
X	0000166	molecular_function	nucleotide binding
X	0003824	molecular_function	catalytic activity
X	0004370	molecular_function	glycerol kinase activity
X	0005515	molecular_function	protein binding
X	0005524	molecular_function	ATP binding
X	0005829	cellular_component	cytosol
X	0005975	biological_process	carbohydrate metabolic process
X	0006071	biological_process	glycerol metabolic process
X	0006072	biological_process	glycerol-3-phosphate metabolic process
X	0006974	biological_process	DNA damage response
X	0008270	molecular_function	zinc ion binding
X	0016301	molecular_function	kinase activity
X	0016310	biological_process	phosphorylation
X	0016740	molecular_function	transferase activity
X	0016773	molecular_function	phosphotransferase activity, alcohol group as acceptor
X	0019563	biological_process	glycerol catabolic process
X	0042802	molecular_function	identical protein binding
X	0046872	molecular_function	metal ion binding
Y	0000166	molecular_function	nucleotide binding
Y	0003824	molecular_function	catalytic activity
Y	0004370	molecular_function	glycerol kinase activity
Y	0005515	molecular_function	protein binding
Y	0005524	molecular_function	ATP binding
Y	0005829	cellular_component	cytosol
Y	0005975	biological_process	carbohydrate metabolic process
Y	0006071	biological_process	glycerol metabolic process
Y	0006072	biological_process	glycerol-3-phosphate metabolic process
Y	0006974	biological_process	DNA damage response
Y	0008270	molecular_function	zinc ion binding
Y	0016301	molecular_function	kinase activity
Y	0016310	biological_process	phosphorylation
Y	0016740	molecular_function	transferase activity
Y	0016773	molecular_function	phosphotransferase activity, alcohol group as acceptor
Y	0019563	biological_process	glycerol catabolic process
Y	0042802	molecular_function	identical protein binding
Y	0046872	molecular_function	metal ion binding
Z	0000166	molecular_function	nucleotide binding
Z	0003824	molecular_function	catalytic activity
Z	0004370	molecular_function	glycerol kinase activity
Z	0005515	molecular_function	protein binding
Z	0005524	molecular_function	ATP binding
Z	0005829	cellular_component	cytosol
Z	0005975	biological_process	carbohydrate metabolic process
Z	0006071	biological_process	glycerol metabolic process
Z	0006072	biological_process	glycerol-3-phosphate metabolic process
Z	0006974	biological_process	DNA damage response
Z	0008270	molecular_function	zinc ion binding
Z	0016301	molecular_function	kinase activity
Z	0016310	biological_process	phosphorylation
Z	0016740	molecular_function	transferase activity
Z	0016773	molecular_function	phosphotransferase activity, alcohol group as acceptor
Z	0019563	biological_process	glycerol catabolic process
Z	0042802	molecular_function	identical protein binding
Z	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 O 502

Chain	Residue
X	HOH506
Z	ARG236
O	ASN228
O	GLY233
O	GLY234
O	ARG236
O	HOH505
X	GLY233
X	GLY234
X	ARG236

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 Z 502

Chain	Residue
O	ARG236
Y	GLY233
Y	GLY234
Y	ARG236
Z	GLY233
Z	GLY234
Z	ARG236

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 O 503

Chain	Residue
O	GLY12
O	THR13
O	THR14
O	ARG17
O	THR267

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 Y 502

Chain	Residue
Y	GLY12
Y	THR13
Y	THR14
Y	ASP245
Y	THR267
Y	GOL503

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 Z 503

Chain	Residue
Z	GLY12
Z	THR13
Z	ARG17
Z	ASP245
Z	THR267
Z	HOH513

site_id	AC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 X 502

Chain	Residue
X	GLY12
X	THR13
X	ARG17
X	ASP245
X	THR267
X	GOL503
X	HOH513
X	HOH526

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL O 504

Chain	Residue
O	ARG83
O	GLU84
O	TRP103
O	TYR135
O	ASP245
O	GLN246

site_id	AC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL Y 503

Chain	Residue
Y	GLN82
Y	ARG83
Y	GLU84
Y	TRP103
Y	TYR135
Y	ASP245
Y	GLN246
Y	SO4502
Y	HOH527

site_id	AC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL Z 504

Chain	Residue
Z	GLN82
Z	ARG83
Z	GLU84
Z	TRP103
Z	TYR135
Z	ASP245
Z	GLN246
Z	PHE270

site_id	BC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL X 503

Chain	Residue
X	GLN82
X	ARG83
X	GLU84
X	TRP103
X	TYR135
X	ASP245
X	GLN246
X	SO4502

site_id	SO4
Number of Residues	1
Details	SULPHATE BINDING SITE. RESIDUES 230 - 236: THIS REGION IS DISORDERED IN PREVIOUSLY SOLVED CRYSTAL STRUCTURES OF GLYCEROL KINASE, BUT IS ORDERED IN THIS STRUCTURE AND FORMS A SULPHATE BINDING SITE AT THE 2-FOLD DIMER-DIMER INTERFACE. THIS SITE IS PROPOSED TO BE PART OF THE BINDING SITE FOR THE ALLOSTERIC EFFECTOR FBP (SEE REF. FOR THIS STRUCTURE).

Chain	Residue
O	ARG236

Functional Information from PROSITE/UniProt

site_id	PS00445
Number of Residues	21
Details	FGGY_KINASES_2 FGGY family of carbohydrate kinases signature 2. GaIFGLtrgvnan.HIIRATLE

Chain	Residue	Details
O	GLY362-GLU382

site_id	PS00933
Number of Residues	13
Details	FGGY_KINASES_1 FGGY family of carbohydrate kinases signature 1. YfSgtKVKWILDH

Chain	Residue	Details
O	TYR135-HIS147

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"PubMed","id":"8170944","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1GLC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GLD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GLE","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10090737","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1BWF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GLJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GLL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10090737","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1GLJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"8170944","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8430315","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9817843","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1GLB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GLD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GLE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GLF","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"9843423","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1BO5","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"8430315","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9843423","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1BO5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1BOT","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10090737","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1BWF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GLL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"8170944","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8430315","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1GLB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GLC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GLD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GLE","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	4
Details	Modified residue: {"description":"N6-malonyllysine","evidences":[{"source":"PubMed","id":"21908771","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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