2ZF5 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HIGHLY THERMOSTABLE GLYCEROL KINASE FROM A HYPERTHERMOPHILIC ARCHAEON

Authors :   Y. Koga, R. Katsumi, D. -J. You, H. Matsumura, K. Takano, S. Kanaya

Date :   20 Dec 07 (Deposition) - 06 May 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : O,Y
Biol. Unit 1: O,Y  (1x)
Biol. Unit 2: O,Y  (3x)

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

Reference :   Y. Koga, R. Katsumi, D. -J. You, H. Matsumura, K. Takano, S. Kanaya
Crystal Structure Of Highly Thermostable Glycerol Kinase From A Hyperthermophilic Archaeon In A Dimeric Form
Febs J. V. 275 2632 2008
PubMed-ID: 18422647 | Reference-DOI: 10.1111/J.1742-4658.2008.06410.X

Molecule 1 - GLYCEROL KINASE
	Chains	:	O, Y
	EC Number	:	2.7.1.30
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET8C
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMOCOCCUS KODAKARENSIS
	Organism Taxid	:	69014
	Strain	:	KOD1

		1	2
Asymmetric Unit	:	O	Y
Biological Unit 1 (1x)	:	O	Y
Biological Unit 2 (3x)	:	O	Y

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2ZF5)

(no "Site" information available for 2ZF5)

(no "SS Bond" information available for 2ZF5)

Asymmetric Unit

No.	Residues
1	Ala O:346	-	Pro O:347
2	Ala Y:346	-	Pro Y:347

(no "SAP(SNP)/Variant" information available for 2ZF5)

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_THEKO	132-144	2	O:132-144 Y:132-144
2	FGGY_KINASES_2	PS00445	FGGY family of carbohydrate kinases signature 2.	GLPK_THEKO	355-375	2	O:355-375 Y:355-375

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_THEKO	132-144	2	O:132-144 Y:132-144
2	FGGY_KINASES_2	PS00445	FGGY family of carbohydrate kinases signature 2.	GLPK_THEKO	355-375	2	O:355-375 Y:355-375

Biological Unit 2 (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FGGY_KINASES_1	PS00933	FGGY family of carbohydrate kinases signature 1.	GLPK_THEKO	132-144	6	O:132-144 Y:132-144
2	FGGY_KINASES_2	PS00445	FGGY family of carbohydrate kinases signature 2.	GLPK_THEKO	355-375	6	O:355-375 Y:355-375

(no "Exon" information available for 2ZF5)

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:494
 aligned with GLPK_THEKO | O93623 from UniProtKB/Swiss-Prot  Length:497

    Alignment length:494
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490    
           GLPK_THEKO     1 MEKFVLSLDEGTTSARAIIFDRESNIHGIGQYEFPQHYPRPGWVEHNPEEIWDAQLRAIKDAIQSARIEPNQIAAIGVTNQRETTLVWDKDGKPLYNAIVWQCRRTAEMVEEIKREYGTMIKEKTGLVPDAYFSASKLKWLLDNVPGLREKAEKGEVMFGTVDTFLIYRLTGEHVTDYSNASRTMLFNIKKLDWDDELLELFDIPESVLPEVRESSEVYGYTKKELLGAEIPVSGDAGDQQAALFGQAAFEAGMVKATYGTGSFILVNTDKMVLYSDNLLTTIAWGLNGRVSYALEGSIFVTGAAVQWLRDGIKIIKHASETEELATKLESNEGVYFVPAFVGLGAPYWDQFARGIIIGITRGTGREHLARATLEAIAYLTRDVVDEMEKLVQIKELRVDGGATANDFLMQFQADILNRKVIRPVVKETTALGAAYLAGLAVDYWADTREIAELWKAERIFEPKMDEKTRERLYKGWKEAVKRAMGWAKVVDSA 494
               SCOP domains d2zf5o1 O:1-247 automated matches                                                                                                                                                                                                                      d2zf5o2 O:248-494 automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...eeeeeee.....eeeeeeee...........eehhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee....eeee.........ee......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhh...eeeehhhhhhhhhhh..eeehhhhh....ee....eehhhhhhhh..hhhhh.eee..eeeeee.hhhhhh...eeeeeeehhhhhhhhh.......eeeee...eeeeeeee.........eeeeeeee..eeeeeeeeee..hhhhhhhhhhh.....hhhhhhhhhh........eee................eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh....hhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh..hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zf5 O   1 MEKFVLSLDEGTTSARAIIFDRESNIHGIGQYEFPQHYPRPGWVEHNPEEIWDAQLRAIKDAIQSARIEPNQIAAIGVTNQRETTLVWDKDGKPLYNAIVWQCRRTAEMVEEIKREYGTMIKEKTGLVPDAYFSASKLKWLLDNVPGLREKAEKGEVMFGTVDTFLIYRLTGEHVTDYSNASRTMLFNIKKLDWDDELLELFDIPESVLPEVRESSEVYGYTKKELLGAEIPVSGDAGDQQAALFGQAAFEAGMVKATYGTGSFILVNTDKMVLYSDNLLTTIAWGLNGRVSYALEGSIFVTGAAVQWLRDGIKIIKHASETEELATKLESNEGVYFVPAFVGLGAPYWDQFARGIIIGITRGTGREHLARATLEAIAYLTRDVVDEMEKLVQIKELRVDGGATANDFLMQFQADILNRKVIRPVVKETTALGAAYLAGLAVDYWADTREIAELWKAERIFEPKMDEKTRERLYKGWKEAVKRAMGWAKVVDSA 494
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490

Chain Y from PDB  Type:PROTEIN  Length:494
 aligned with GLPK_THEKO | O93623 from UniProtKB/Swiss-Prot  Length:497

    Alignment length:494
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490    
           GLPK_THEKO     1 MEKFVLSLDEGTTSARAIIFDRESNIHGIGQYEFPQHYPRPGWVEHNPEEIWDAQLRAIKDAIQSARIEPNQIAAIGVTNQRETTLVWDKDGKPLYNAIVWQCRRTAEMVEEIKREYGTMIKEKTGLVPDAYFSASKLKWLLDNVPGLREKAEKGEVMFGTVDTFLIYRLTGEHVTDYSNASRTMLFNIKKLDWDDELLELFDIPESVLPEVRESSEVYGYTKKELLGAEIPVSGDAGDQQAALFGQAAFEAGMVKATYGTGSFILVNTDKMVLYSDNLLTTIAWGLNGRVSYALEGSIFVTGAAVQWLRDGIKIIKHASETEELATKLESNEGVYFVPAFVGLGAPYWDQFARGIIIGITRGTGREHLARATLEAIAYLTRDVVDEMEKLVQIKELRVDGGATANDFLMQFQADILNRKVIRPVVKETTALGAAYLAGLAVDYWADTREIAELWKAERIFEPKMDEKTRERLYKGWKEAVKRAMGWAKVVDSA 494
               SCOP domains d2zf5y1 Y:1-247 automated matches                                                                                                                                                                                                                      d2zf5y2 Y:248-494 automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...eeeeeee.....eeeeeeee...........eehhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee.....eeee........ee......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhh..eeeehhhhhhhhhhhh..eeehhhhhh...ee....eehhhhhhhh..hhhhh.eee..eeeeee.hhhhhh...eeeeeeehhhhhhhhh.......eeeee...eeeeeeee.........eeeeeeee..eeeeeeeeee..hhhhhhhhhhh.....hhhhhhhhhh........eee................eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhh.....hhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zf5 Y   1 MEKFVLSLDEGTTSARAIIFDRESNIHGIGQYEFPQHYPRPGWVEHNPEEIWDAQLRAIKDAIQSARIEPNQIAAIGVTNQRETTLVWDKDGKPLYNAIVWQCRRTAEMVEEIKREYGTMIKEKTGLVPDAYFSASKLKWLLDNVPGLREKAEKGEVMFGTVDTFLIYRLTGEHVTDYSNASRTMLFNIKKLDWDDELLELFDIPESVLPEVRESSEVYGYTKKELLGAEIPVSGDAGDQQAALFGQAAFEAGMVKATYGTGSFILVNTDKMVLYSDNLLTTIAWGLNGRVSYALEGSIFVTGAAVQWLRDGIKIIKHASETEELATKLESNEGVYFVPAFVGLGAPYWDQFARGIIIGITRGTGREHLARATLEAIAYLTRDVVDEMEKLVQIKELRVDGGATANDFLMQFQADILNRKVIRPVVKETTALGAAYLAGLAVDYWADTREIAELWKAERIFEPKMDEKTRERLYKGWKEAVKRAMGWAKVVDSA 494
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490

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: automated matches (111)

Protein domain: automated matches (111)

Thermococcus kodakarensis [TaxId: 69014] (1)

1a	d2zf5o1	O:1-247
1b	d2zf5o2	O:248-494
1c	d2zf5y1	Y:1-247
1d	d2zf5y2	Y:248-494

(no "CATH Domain" information available for 2ZF5)

(no "Pfam Domain" information available for 2ZF5)

Asymmetric Unit(hide GO term definitions)

Chain O,Y (GLPK_THEKO | O93623)

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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2zf5)

	Sites
(no "Sites" information available for 2zf5)

	Cis Peptide Bonds
		Ala O:346 - Pro O:347	[ RasMol ]
		Ala Y:346 - Pro Y:347	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2zf5
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Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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