3H3N - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   GLYCEROL KINASE H232R WITH GLYCEROL

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

Date :   16 Apr 09 (Deposition) - 02 Jun 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.73

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, 10)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	2	Ligand/Ion	GLYCEROL
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	2	Ligand/Ion	GLYCEROL
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (3, 20)

No.	Name	Count	Type	Full Name
1	EDO	12	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	4	Ligand/Ion	GLYCEROL
3	PO4	4	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG X:84 , GLU X:85 , TRP X:104 , TYR X:136 , ASP X:246 , GLN X:247 , PHE X:271 , PO4 X:507	BINDING SITE FOR RESIDUE GOL X 1000
02	AC2	SOFTWARE	SER O:59 , ALA O:62 , EDO O:3124 , SER X:59 , HOH X:526 , HOH X:611 , EDO X:3123	BINDING SITE FOR RESIDUE EDO X 3122
03	AC3	SOFTWARE	HOH O:593 , SER X:32 , GLN X:33 , SER X:59 , HOH X:609 , EDO X:3122	BINDING SITE FOR RESIDUE EDO X 3123
04	AC4	SOFTWARE	TRP X:54 , GLN X:58 , ARG X:232 , TYR X:234 , HOH X:593	BINDING SITE FOR RESIDUE EDO X 3125
05	AC5	SOFTWARE	THR X:14 , GLY X:267 , THR X:268 , HOH X:519 , HOH X:544 , HOH X:555 , GOL X:1000	BINDING SITE FOR RESIDUE PO4 X 507
06	AC6	SOFTWARE	ARG O:84 , GLU O:85 , TRP O:104 , TYR O:136 , ASP O:246 , GLN O:247 , PHE O:271 , PO4 O:507 , HOH O:629	BINDING SITE FOR RESIDUE GOL O 1001
07	AC7	SOFTWARE	SER O:32 , GLN O:33 , SER O:59 , HOH O:593 , HOH X:609 , EDO X:3122	BINDING SITE FOR RESIDUE EDO O 3124
08	AC8	SOFTWARE	ALA O:310 , GLY O:311 , LEU O:382 , ALA O:413 , HOH O:642	BINDING SITE FOR RESIDUE EDO O 3126
09	AC9	SOFTWARE	GLN O:383 , PHE O:422	BINDING SITE FOR RESIDUE EDO O 3127
10	BC1	SOFTWARE	GLY O:13 , THR O:14 , THR O:268 , HOH O:533 , HOH O:629 , GOL O:1001	BINDING SITE FOR RESIDUE PO4 O 507

(no "SS Bond" information available for 3H3N)

Asymmetric Unit

No.	Residues
1	Ala X:354	-	Pro X:355
2	Ala O:354	-	Pro O:355

(no "SAP(SNP)/Variant" information available for 3H3N)

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 3H3N)

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:501
 aligned with GLPK_ENTCA | O34153 from UniProtKB/Swiss-Prot  Length:506

    Alignment length:501
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501 
           GLPK_ENTCA     2 AEKNYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYHFYGSEVPIAGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVYYALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNLYEGWKQAVAATQTFKFKAK 502
               SCOP domains d3h3no1 O:2-254 Glycerol kinase                                                                                                                                                                                                                              d3h3no2 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.......hhhhhhhh........eee.................eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhh....hhhhhhhh.....ee....hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h3n O   2 AEKNYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYRFYGSEVPIAGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVYYALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNLYEGWKQAVAATQTFKFKAK 502
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501

Chain X from PDB  Type:PROTEIN  Length:501
 aligned with GLPK_ENTCA | O34153 from UniProtKB/Swiss-Prot  Length:506

    Alignment length:501
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501 
           GLPK_ENTCA     2 AEKNYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYHFYGSEVPIAGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVYYALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNLYEGWKQAVAATQTFKFKAK 502
               SCOP domains d3h3nx1 X:2-254 Glycerol kinase                                                                                                                                                                                                                              d3h3nx2 X:255-502 Glycerol kinase                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...eeeeeeee....eeeeeeee...........eehhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.....eeee.........ee......hhhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhh..eeeehhhhhhhhhhh.....eeehhhhhh...ee....eehhhhhhhh..hhhhh.eee..eeeeee.hhhhh.....eeeeeeehhhhhhhhh.......eeeee...eeeeeeee..........eeeeeeee..eeeeeeeeee...hhhhhhhhhh.......hhhhhhhh........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
                 3h3n X   2 AEKNYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYRFYGSEVPIAGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVYYALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNLYEGWKQAVAATQTFKFKAK 502
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501

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	d3h3no1	O:2-254
1b	d3h3no2	O:255-502
1c	d3h3nx1	X:2-254
1d	d3h3nx2	X:255-502

(no "CATH Domain" information available for 3H3N)

(no "Pfam Domain" information available for 3H3N)

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 ]

Biological Units
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	3h3n
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	2.7.1.30
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	GLPK_ENTCA \| O34153	:	1r59 1xup 3d7e 3flc 3h3o 3h45 3h46

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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