3H46 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   GLYCEROL KINASE H232E WITH GLYCEROL

Authors :   J. I. Yeh, R. D. Kettering

Date :   17 Apr 09 (Deposition) - 02 Jun 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym. Unit : O,X
Biol. Unit 1: O,X  (1x)
Biol. Unit 2: O,X  (2x)

Keywords :   Glycerol, Kinase, Atp-Binding, Glycerol Metabolism, Nucleotide- Binding, Phosphoprotein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. I. Yeh, R. Kettering, R. Saxl, A. Bourand, E. Darbon, N. Joly, P. Briozzo, J. Deutscher
Structural Characterizations Of Glycerol Kinase: Unraveling Phosphorylation-Induced Long-Range Activation
Biochemistry V. 48 346 2009
PubMed-ID: 19102629 | Reference-DOI: 10.1021/BI8009407

Molecule 1 - GLYCEROL KINASE
	Chains	:	X, O
	EC Number	:	2.7.1.30
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	POXO4
	Expression System Strain	:	JM109(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GLPK
	Mutation	:	YES
	Organism Common	:	ENTEROCOCCUS FLAVESCENS
	Organism Scientific	:	ENTEROCOCCUS CASSELIFLAVUS
	Organism Taxid	:	37734

		1	2
Asymmetric Unit	:	O	X
Biological Unit 1 (1x)	:	O	X
Biological Unit 2 (2x)	:	O	X

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	2	Ligand/Ion	GLYCEROL
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	2	Ligand/Ion	GLYCEROL
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	4	Ligand/Ion	GLYCEROL
3	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR X:14 , THR X:15 , GLY X:267 , THR X:268 , GOL X:1001	BINDING SITE FOR RESIDUE SO4 X 507
2	AC2	SOFTWARE	ARG X:84 , GLU X:85 , TRP X:104 , TYR X:136 , ASP X:246 , GLN X:247 , PHE X:271 , SO4 X:507 , HOH X:569	BINDING SITE FOR RESIDUE GOL X 1001
3	AC3	SOFTWARE	EDO O:3123 , SER X:32 , SER X:59	BINDING SITE FOR RESIDUE EDO X 3122
4	AC4	SOFTWARE	THR O:14 , THR O:15 , GLY O:267 , THR O:268 , HOH O:564	BINDING SITE FOR RESIDUE SO4 O 507
5	AC5	SOFTWARE	ARG O:84 , GLU O:85 , TRP O:104 , TYR O:136 , ASP O:246 , GLN O:247 , PHE O:271 , HOH O:564	BINDING SITE FOR RESIDUE GOL O 1000
6	AC6	SOFTWARE	SER O:32 , SER O:59 , EDO X:3122	BINDING SITE FOR RESIDUE EDO O 3123

(no "SS Bond" information available for 3H46)

Asymmetric Unit

No.	Residues
1	Gly X:235	-	Ser X:236
2	Ala X:354	-	Pro X:355
3	Ala O:354	-	Pro O:355

(no "SAP(SNP)/Variant" information available for 3H46)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FGGY_KINASES_1	PS00933	FGGY family of carbohydrate kinases signature 1.	GLPK_ENTCA	136-148	2	O:136-148 X:136-148
2	FGGY_KINASES_2	PS00445	FGGY family of carbohydrate kinases signature 2.	GLPK_ENTCA	363-383	2	O:363-383 X:363-383

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FGGY_KINASES_1	PS00933	FGGY family of carbohydrate kinases signature 1.	GLPK_ENTCA	136-148	2	O:136-148 X:136-148
2	FGGY_KINASES_2	PS00445	FGGY family of carbohydrate kinases signature 2.	GLPK_ENTCA	363-383	2	O:363-383 X:363-383

Biological Unit 2 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FGGY_KINASES_1	PS00933	FGGY family of carbohydrate kinases signature 1.	GLPK_ENTCA	136-148	4	O:136-148 X:136-148
2	FGGY_KINASES_2	PS00445	FGGY family of carbohydrate kinases signature 2.	GLPK_ENTCA	363-383	4	O:363-383 X:363-383

(no "Exon" information available for 3H46)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain O from PDB  Type:PROTEIN  Length:500
 aligned with GLPK_ENTCA | O34153 from UniProtKB/Swiss-Prot  Length:506

    Alignment length:500
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502
           GLPK_ENTCA     3 EKNYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYHFYGSEVPIAGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVYYALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNLYEGWKQAVAATQTFKFKAK 502
               SCOP domains d3h46o1 O:3-254 Glycerol kinase                                                                                                                                                                                                                             d3h46o2 O:255-502 Glycerol kinase                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...eeeeeeee....eeeeeeee...........eehhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee....eeeee.........ee......hhhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhh..eeeeehhhhhhhhhh.....eeehhhhhh...ee....eehhhhhhhh..hhhhh.eee..eeeeee...........eeeeeeehhhhhhhhh.......eeeee...eeeeeeee..........eeeeeeee..eeeeeeeeee..hhhhhhhhhhh.......hhhhhhhhh.......eee.................eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhh....hhhhhhh......ee....hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h46 O   3 EKNYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYEFYGSEVPIAGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVYYALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNLYEGWKQAVAATQTFKFKAK 502
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502

Chain X from PDB  Type:PROTEIN  Length:500
 aligned with GLPK_ENTCA | O34153 from UniProtKB/Swiss-Prot  Length:506

    Alignment length:500
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502
           GLPK_ENTCA     3 EKNYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYHFYGSEVPIAGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVYYALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNLYEGWKQAVAATQTFKFKAK 502
               SCOP domains d3h46x1 X:3-254 Glycerol kinase                                                                                                                                                                                                                             d3h46x2 X:255-502 Glycerol kinase                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...eeeeeeee....eeeeeeee...........eehhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee....eeeee.........ee......hhhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhh..eeeeehhhhhhhhhh.....eeehhhhhh...ee....eehhhhhhhh..hhhhh.eee..eeeeee...........eeeeeeehhhhhhhhh.......eeeee...eeeeeeee..........eeeeeeee..eeeeeeeeee..hhhhhhhhhhh.......hhhhhhhhh.......eee.................eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhh....hhhhhhh......ee....hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h46 X   3 EKNYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYEFYGSEVPIAGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVYYALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNLYEGWKQAVAATQTFKFKAK 502
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Ribonuclease H-like motif (1424)

Superfamily: Actin-like ATPase domain (426)

Family: Glycerol kinase (21)

Protein domain: Glycerol kinase (21)

Enterococcus casseliflavus [TaxId: 37734] (8)

1a	d3h46o1	O:3-254
1b	d3h46o2	O:255-502
1c	d3h46x1	X:3-254
1d	d3h46x2	X:255-502

(no "CATH Domain" information available for 3H46)

(no "Pfam Domain" information available for 3H46)

Asymmetric Unit(hide GO term definitions)

Chain O,X (GLPK_ENTCA | O34153)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004370	glycerol kinase activity	Catalysis of the reaction: ATP + glycerol = sn-glycerol 3-phosphate + ADP + 2 H(+).
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016773	phosphotransferase activity, alcohol group as acceptor	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0019563	glycerol catabolic process	The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
	GO:0006071	glycerol metabolic process	The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
	GO:0006072	glycerol-3-phosphate metabolic process	The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala O:354 - Pro O:355	[ RasMol ]
		Ala X:354 - Pro X:355	[ RasMol ]
		Gly X:235 - Ser X:236	[ RasMol ]

Biological Units
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Access by PDB/NDB ID
	3h46
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	2.7.1.30
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		Domain Information	:	XDom
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	GLPK_ENTCA \| O34153	:	1r59 1xup 3d7e 3flc 3h3n 3h3o 3h45

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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