1R59 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   ENTEROCOCCUS CASSELIFLAVUS GLYCEROL KINASE

Authors :   J. I. Yeh, V. Charrier, J. Paulo, L. Hou, E. Darbon, A. Claiborne, W. G. Hol, J. Deutscher

Date :   09 Oct 03 (Deposition) - 12 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : O,X

Keywords :   Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. I. Yeh, V. Charrier, J. Paulo, L. Hou, E. Darbon, A. Claiborne, W. G. Hol, J. Deutscher
Structures Of Enterococcal Glycerol Kinase In The Absence And Presence Of Glycerol: Correlation Of Conformation To Substrate Binding And A Mechanism Of Activation By Phosphorylation
Biochemistry V. 43 362 2004
PubMed-ID: 14717590 | Reference-DOI: 10.1021/BI034258O
(for further references see the PDB file header)

Molecule 1 - GLYCEROL KINASE
	Chains	:	O, X
	EC Number	:	2.7.1.30
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	POXO4
	Expression System Strain	:	JM109DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	GLYCEROL KINASE
	Gene	:	GLPK
	Organism Scientific	:	ENTEROCOCCUS CASSELIFLAVUS
	Organism Taxid	:	37734

		1	2
Asymmetric/Biological Unit	:	O	X

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1R59)

(no "Site" information available for 1R59)

(no "SS Bond" information available for 1R59)

(no "Cis Peptide Bond" information available for 1R59)

(no "SAP(SNP)/Variant" information available for 1R59)

Asymmetric/Biological 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

(no "Exon" information available for 1R59)

Asymmetric/Biological 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:480
 aligned with GLPK_ENTCA | O34153 from UniProtKB/Swiss-Prot  Length:506

    Alignment length:487
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       
           GLPK_ENTCA     5 NYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYHFYGSEVPIAGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVYYALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNLYEGWKQAV 491
               SCOP domains d1r59o1 O:5-256 Glycerol kinase                                                                                                                                                                                                                             d1r59o2 O:257-491 Glycerol kinase                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..........ee..........................hhhhh.......hhhhhh........eeeeee.............................hhhhhhhhhhhhhhhhh..........hhhhhhhhhhh.................hhhhhhhhh.......eehhhhhh............hhhhhh..........ee............-------..eeee.....hhhhhh..........ee...ee.eee............eeee.........eeee......hhhhhhh........hhhhhh............eee.................eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhh.......hhhhh.eeeee.......hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r59 O   5 NYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRS-------VPIAGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVYYALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNLYEGWKQAV 491
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224     |   -   |   244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       
                                                                                                                                                                                                                                                           230     238

Chain X from PDB  Type:PROTEIN  Length:480
 aligned with GLPK_ENTCA | O34153 from UniProtKB/Swiss-Prot  Length:506

    Alignment length:487
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       
           GLPK_ENTCA     5 NYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYHFYGSEVPIAGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVYYALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNLYEGWKQAV 491
               SCOP domains d1r59x1 X:5-256 Glycerol kinase                                                                                                                                                                                                                             d1r59x2 X:257-491 Glycerol kinase                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -FGGY_N-1r59X03 X:6-253                                                                                                                                                                                                                                  --------FGGY_C-1r59X01 X:262-452                                                                                                                                                                       --------------------------------------- Pfam domains (1)
           Pfam domains (2) -FGGY_N-1r59X04 X:6-253                                                                                                                                                                                                                                  --------FGGY_C-1r59X02 X:262-452                                                                                                                                                                       --------------------------------------- Pfam domains (2)
         Sec.struct. author ..........................................ee.hhhhhhhhhhhhhhhh........................ee.........ee...........hhhhhhhhhhhhh...........hhhhhhhhhhhh...........ee...hhhhhhhh.......ee...hhhhh..........hhhhhhhh........ee............-------.......................ee.ee.......eee............eee...........eee.......................................................................hhhhhh.....hhhhhhhh..............eehhhhh..hhhhh.......................hhhhh..............................hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r59 X   5 NYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRS-------VPIAGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVYYALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNLYEGWKQAV 491
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224     |   -   |   244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       
                                                                                                                                                                                                                                                           230     238

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/Biological 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	d1r59o1	O:5-256
1b	d1r59o2	O:257-491
1c	d1r59x1	X:5-256
1d	d1r59x2	X:257-491

(no "CATH Domain" information available for 1R59)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Actin_ATPase (173)

Family: FGGY_C (10)

Enterococcus casseliflavus (Enterococcus flavescens) (2)

1a	FGGY_C-1r59X01	X:262-452
1b	FGGY_C-1r59X02	X:262-452

Family: FGGY_N (10)

Enterococcus casseliflavus (Enterococcus flavescens) (2)

2a	FGGY_N-1r59X03	X:6-253
2b	FGGY_N-1r59X04	X:6-253

Asymmetric/Biological 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/Biological Unit
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1r5f	ENTEROCOCCUS CASSELIFLAVUS GLYCEROL KINASE COMPLEXED WITH GLYCEROL

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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PROSITE Motifs (2, 4)

Exons (0, 0)

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SCOP Domains (1, 4)

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Gene Ontology (11, 11)

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