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Asym./Biol. Unit (Jmol Viewer)

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Title :   X-RAY STRUCTURE OF HUMAN N-ACETYL GALACTOSAMINE KINASE COMPLEXED WITH MG-ADP AND N-ACETYL GALACTOSAMINE 1-PHOSPHATE

Authors :   J. B. Thoden, H. M. Holden

Date :   22 Jun 05 (Deposition) - 26 Jul 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym./Biol. Unit : A

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

Reference :   J. B. Thoden, H. M. Holden
The Molecular Architecture Of Human N-Acetylgalactosamine Kinase.
J. Biol. Chem. V. 280 32784 2005
PubMed-ID: 16006554 | Reference-DOI: 10.1074/JBC.M505730200
(for further references see the PDB file header)

Molecule 1 - N-ACETYLGALACTOSAMINE KINASE
	Chains	:	A
	EC Number	:	2.7.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	HMS174(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GALK2, GK2
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GALNAC KINASE, GALACTOKINASE 2

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 5)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CL	1	Ligand/Ion	CHLORIDE ION
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	NA	1	Ligand/Ion	SODIUM ION
5	NG1	1	Ligand/Ion	N-ACETYL-ALPHA-D-GALACTOSAMINE 1-PHOSPHATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:43 , GLU A:49 , HIS A:50 , ASP A:52 , TYR A:53 , GLY A:143 , SER A:145 , SER A:148 , GLU A:179 , GLY A:186 , GLY A:187 , MET A:189 , ASP A:190 , GLN A:191 , LYS A:234 , PHE A:240 , GLY A:401 , ALA A:402 , MG A:460 , ADP A:463 , HOH A:471 , HOH A:480 , HOH A:545 , HOH A:547 , HOH A:563	BINDING SITE FOR RESIDUE NG1 A 459
2	AC2	SOFTWARE	SER A:147 , NG1 A:459 , ADP A:463 , HOH A:470 , HOH A:471	BINDING SITE FOR RESIDUE MG A 460
3	AC3	SOFTWARE	TRP A:107 , HOH A:644 , HOH A:653	BINDING SITE FOR RESIDUE CL A 461
4	AC4	SOFTWARE	PHE A:207 , SER A:208 , ARG A:211 , HOH A:626 , HOH A:833 , HOH A:871	BINDING SITE FOR RESIDUE NA A 462
5	AC5	SOFTWARE	ASN A:83 , TYR A:88 , TRP A:107 , TYR A:110 , GLY A:136 , SER A:141 , SER A:142 , GLY A:143 , SER A:145 , SER A:146 , SER A:147 , LEU A:150 , MET A:232 , ASN A:233 , LYS A:234 , NG1 A:459 , MG A:460 , HOH A:471 , HOH A:472 , HOH A:501 , HOH A:530 , HOH A:531 , HOH A:652 , HOH A:653 , HOH A:724	BINDING SITE FOR RESIDUE ADP A 463

(no "SS Bond" information available for 2A2C)

Asymmetric/Biological Unit

No.	Residues
1	Ser A:208	-	Pro A:209

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_049123	I	182	V	GALK2_HUMAN	Polymorphism	35507772	A	I	182	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALACTOKINASE	PS00106	Galactokinase signature.	GALK2_HUMAN	42-53	1	A:42-53
2	GHMP_KINASES_ATP	PS00627	GHMP kinases putative ATP-binding domain.	GALK2_HUMAN	138-149	1	A:138-149

(no "Exon" information available for 2A2C)

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
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Chain A from PDB  Type:PROTEIN  Length:446
 aligned with GALK2_HUMAN | Q01415 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:457
                                    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       
          GALK2_HUMAN     2 ATESPATRRVQVAEHPRLLKLKEMFNSKFGSIPKFYVRAPGRVNIIGEHIDYCGYSVLPMAVEQDVLIAVEPVKTYALQLANTNPLYPDFSTSANNIQIDKTKPLWHNYFLCGLKGIQEHFGLSNLTGMNCLVDGNIPPSSGLSSSSALVCCAGLVTLTVLGRNLSKVELAEICAKSERYIGTEGGGMDQSISFLAEEGTAKLIEFSPLRATDVKLPSGAVFVIANSCVEMNKAATSHFNIRVMECRLAAKLLAKYKSLQWDKVLRLEEVQAKLGISLEEMLLVTEDALHPEPYNPEEICRCLGISLEELRTQILSPNTQDVLIFKLYQRAKHVYSEAARVLQFKKICEEAPENMVQLLGELMNQSHMSCRDMYECSCPELDQLVDICRKFGAQGSRLTGAGWGGCTVSMVPADKLPSFLANVHKAYYQRSDGSLAPEKQSLFATKPGGGALVLLEA 458
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeehhhhhhhhhhhhhhhhhhhh....eeeeeeeeeeee...hhhhh...eeeeeeeeeeeeeee.....eeeee.......eee....--......hhhhhhhhhhhhhhhhh.......eeeeeee........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhh....eeeee....eeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...eeee.......eeeeeee..hhhhhhhhhhhhhhh---------...eeee......eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------GALACTOKINAS------------------------------------------------------------------------------------GHMP_KINASES--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a2c A   2 ATESPATRRVQVAEHPRLLKLKEMFNSKFGSIPKFYVRAPGRVNIIGEHIDYCGYSVLPMAVEQDVLIAVEPVKTYALQLANTNPLYPDFSTSANN--IDKTKPLWHNYFLCGLKGIQEHFGLSNLTGMNCLVDGNIPPSSGLSSSSALVCCAGLVTLTVLGRNLSKVELAEICAKSERYIGTEGGGMDQSISFLAEEGTAKLIEFSPLRATDVKLPSGAVFVIANSCVEMNKAATSHFNIRVMECRLAAKLLAKYKSLQWDKVLRLEEVQAKLGISLEEMLLVTEDALHPEPYNPEEICRCLGISLEELRTQILSPNTQDVLIFKLYQRAKHVYSEAARVLQFKKICEEAPENMVQLLGELMNQSHMSCRDMYECSCPELDQLVDICRKFGAQGSRLTGAGWGGCTVSMVPADKLPSFLANVHKAYYQ---------KQSLFATKPGGGALVLLEA 458
                                    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        |-       441       451       
                                                                                                                          97  |                                                                                                                                                                                                                                                                                                                                       430       440                  
                                                                                                                            100

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 '\|'

(no "SCOP Domain" information available for 2A2C)

(no "CATH Domain" information available for 2A2C)

(no "Pfam Domain" information available for 2A2C)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (GALK2_HUMAN | Q01415)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0033858	N-acetylgalactosamine kinase activity	Catalysis of the reaction: ATP + N-acetyl-D-galactosamine = ADP + N-acetyl-alpha-D-galactosamine 1-phosphate.
	GO:0004335	galactokinase activity	Catalysis of the reaction: D-galactose + ATP = alpha-D-galactose 1-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:0046835	carbohydrate phosphorylation	The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y.
	GO:0006012	galactose metabolic process	The chemical reactions and pathways involving galactose, the aldohexose galacto-hexose. D-galactose is widely distributed in combined form in plants, animals and microorganisms as a constituent of oligo- and polysaccharides; it also occurs in galactolipids and as its glucoside in lactose and melibiose.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ser A:208 - Pro A:209	[ RasMol ]

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	2a2c
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2a2c	X-RAY STRUCTURE OF HUMAN N-ACETYL GALACTOSAMINE KINASE COMPLEXED WITH MG-ADP AND N-ACETYL GALACTOSAMINE 1- PHOSPHATE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (2, 2)

Exons (0, 0)

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Gene Ontology (13, 13)

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