2AJ4 - JenaLib

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Title :   CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE GALACTOKINASE IN COMPLEX WITH GALACTOSE AND MG:AMPPNP

Authors :   J. B. Thoden, C. A. Sellick, D. J. Timson, R. J. Reece, H. M. Holden

Date :   01 Aug 05 (Deposition) - 30 Aug 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

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

Reference :   J. B. Thoden, C. A. Sellick, D. J. Timson, R. J. Reece, H. M. Holden
Molecular Structure Of Saccharomyces Cerevisiae Gal1P, A Bifunctional Galactokinase And Transcriptional Inducer
J. Biol. Chem. V. 280 36905 2005
PubMed-ID: 16115868 | Reference-DOI: 10.1074/JBC.M508446200
(for further references see the PDB file header)

Molecule 1 - GALACTOKINASE
	Chains	:	A, B
	EC Number	:	2.7.1.6
	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	:	GAL1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	GALACTOSE KINASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	CL	2	Ligand/Ion	CHLORIDE ION
3	GLA	2	Ligand/Ion	ALPHA D-GALACTOSE
4	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GLA	1	Ligand/Ion	ALPHA D-GALACTOSE
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GLA	1	Ligand/Ion	ALPHA D-GALACTOSE
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:53 , GLU A:59 , HIS A:60 , ASP A:62 , TYR A:63 , ASN A:213 , GLY A:214 , ASP A:217 , LYS A:266 , TYR A:274 , ALA A:468 , HOH A:566 , HOH A:571	BINDING SITE FOR RESIDUE GLA A 529
2	AC2	SOFTWARE	ARG B:53 , GLU B:59 , HIS B:60 , ASP B:62 , TYR B:63 , ASN B:213 , GLY B:214 , ASP B:217 , LYS B:266 , TYR B:274 , ALA B:468 , HOH B:551 , HOH B:555	BINDING SITE FOR RESIDUE GLA B 529
3	AC3	SOFTWARE	SER A:264 , ANP A:532 , HOH A:565 , HOH A:566	BINDING SITE FOR RESIDUE MG A 530
4	AC4	SOFTWARE	SER B:264 , ANP B:532 , HOH B:550	BINDING SITE FOR RESIDUE MG B 530
5	AC5	SOFTWARE	TYR B:113 , VAL B:114 , LEU B:131 , HIS B:132 , HIS B:135	BINDING SITE FOR RESIDUE CL B 531
6	AC6	SOFTWARE	TYR A:113 , VAL A:114 , LEU A:131 , HIS A:135	BINDING SITE FOR RESIDUE CL A 531
7	AC7	SOFTWARE	MET A:77 , ASN A:95 , TRP A:123 , TYR A:126 , THR A:164 , GLY A:165 , SER A:166 , GLY A:167 , LEU A:168 , SER A:169 , SER A:170 , SER A:171 , PHE A:174 , SER A:264 , ASN A:265 , LYS A:266 , MG A:530 , HOH A:563 , HOH A:566 , HOH A:567	BINDING SITE FOR RESIDUE ANP A 532
8	AC8	SOFTWARE	GLN A:386 , MET B:77 , ASN B:95 , TRP B:123 , TYR B:126 , THR B:164 , GLY B:165 , SER B:166 , GLY B:167 , LEU B:168 , SER B:169 , SER B:170 , SER B:171 , PHE B:174 , SER B:264 , ASN B:265 , LYS B:266 , MG B:530 , HOH B:547 , HOH B:548 , HOH B:552	BINDING SITE FOR RESIDUE ANP B 532

(no "SS Bond" information available for 2AJ4)

Asymmetric Unit

No.	Residues
1	Lys A:235	-	Pro A:236
2	Lys B:235	-	Pro B:236

(no "SAP(SNP)/Variant" information available for 2AJ4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALACTOKINASE	PS00106	Galactokinase signature.	GAL1_YEAST	52-63	2	A:52-63 B:52-63
2	GHMP_KINASES_ATP	PS00627	GHMP kinases putative ATP-binding domain.	GAL1_YEAST	162-173	2	A:162-173 B:162-173

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALACTOKINASE	PS00106	Galactokinase signature.	GAL1_YEAST	52-63	1	A:52-63 -
2	GHMP_KINASES_ATP	PS00627	GHMP kinases putative ATP-binding domain.	GAL1_YEAST	162-173	1	A:162-173 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALACTOKINASE	PS00106	Galactokinase signature.	GAL1_YEAST	52-63	1	- B:52-63
2	GHMP_KINASES_ATP	PS00627	GHMP kinases putative ATP-binding domain.	GAL1_YEAST	162-173	1	- B:162-173

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YBR020W	1	YBR020W.1	II:279021-280607	1587	GAL1_YEAST	1-528	528	2	A:9-528 (gaps) B:9-528 (gaps)	520 520

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 A from PDB  Type:PROTEIN  Length:509
 aligned with GAL1_YEAST | P04385 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:520
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528
           GAL1_YEAST     9 VIVPEFNSSAKELPRPLAEKCPSIIKKFISAYDAKPDFVARSPGRVNLIGEHIDYCDFSVLPLAIDFDMLCAVKVLNEKNPSITLINADPKFAQRKFDLPLDGSYVTIDPSVSDWSNYFKCGLHVAHSFLKKLAPERFASAPLAGLQVFCEGDVPTGSGLSSSAAFICAVALAVVKANMGPGYHMSKQNLMRITVVAEHYVGVNNGGMDQAASVCGEEDHALYVEFKPQLKATPFKFPQLKNHEISFVIANTLVVSNKFETAPTNYNLRVVEVTTAANVLAATYGVVLLSGKEGSSTNKGNLRDFMNVYYARYHNISTPWNGDIESGIERLTKMLVLVEESLANKKQGFSVDDVAQSLNCSREEFTRDYLTTSPVRFQVLKLYQRAKHVYSESLRVLKAVKLMTTASFTADEDFFKQFGALMNESQASCDKLYECSCPEIDKICSIALSNGSYGSRLTGAGWGGCTVHLVPGGPNGNIEKVKEALANEFYKVKYPKITDAELENAIIVSKPALGSCLYEL 528
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....-..hhhhhhhhhhhhhhhhhhhh....eeeeeeeeeeee...hhhhh...eeeeeeeeeeeeeeee.....eeeeee.......eeee...............hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee........hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhhh....eeeee.....eeeee........eeeeeeee.............hhhhhhhhhhhhhhhhhhhh.....--------...hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh--..hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...eeee.......eeeeeeee....hhhhhhhhhhhhhhhhhh...hhhhhhhheeee......eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------GALACTOKINAS--------------------------------------------------------------------------------------------------GHMP_KINASES------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:9-528 (gaps) UniProt: 1-528 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Transcript 1
                 2aj4 A   9 VIVPEFNSSA-ELPRPLAEKCPSIIKKFISAYDAKPDFVARSPGRVNLIGEHIDYCDFSVLPLAIDFDMLCAVKVLNEKNPSITLINADPKFAQRKFDLPLDGSYVTIDPSVSDWSNYFKCGLHVAHSFLKKLAPERFASAPLAGLQVFCEGDVPTGSGLSSSAAFICAVALAVVKANMGPGYHMSKQNLMRITVVAEHYVGVNNGGMDQAASVCGEEDHALYVEFKPQLKATPFKFPQLKNHEISFVIANTLVVSNKFETAPTNYNLRVVEVTTAANVLAATYGVVLL--------NKGNLRDFMNVYYARYHNISTPWNGDIESGIERLTKMLVLVEESLANKKQGFSVDDVAQSLNCSREEFTRDYLTTSPVRFQVLKLYQRAKHVYSESLRVLKAVKLMTT--FTADEDFFKQFGALMNESQASCDKLYECSCPEIDKICSIALSNGSYGSRLTGAGWGGCTVHLVPGGPNGNIEKVKEALANEFYKVKYPKITDAELENAIIVSKPALGSCLYEL 528
                                    18 |      28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288        |-       308       318       328       338       348       358       368       378       388       398       408    |  418       428       438       448       458       468       478       488       498       508       518       528
                                    18 |                                                                                                                                                                                                                                                                                  297      306                                                                                                        413  |                                                                                                                
                                      20                                                                                                                                                                                                                                                                                                                                                                                                         416

Chain B from PDB  Type:PROTEIN  Length:505
 aligned with GAL1_YEAST | P04385 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:520
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528
           GAL1_YEAST     9 VIVPEFNSSAKELPRPLAEKCPSIIKKFISAYDAKPDFVARSPGRVNLIGEHIDYCDFSVLPLAIDFDMLCAVKVLNEKNPSITLINADPKFAQRKFDLPLDGSYVTIDPSVSDWSNYFKCGLHVAHSFLKKLAPERFASAPLAGLQVFCEGDVPTGSGLSSSAAFICAVALAVVKANMGPGYHMSKQNLMRITVVAEHYVGVNNGGMDQAASVCGEEDHALYVEFKPQLKATPFKFPQLKNHEISFVIANTLVVSNKFETAPTNYNLRVVEVTTAANVLAATYGVVLLSGKEGSSTNKGNLRDFMNVYYARYHNISTPWNGDIESGIERLTKMLVLVEESLANKKQGFSVDDVAQSLNCSREEFTRDYLTTSPVRFQVLKLYQRAKHVYSESLRVLKAVKLMTTASFTADEDFFKQFGALMNESQASCDKLYECSCPEIDKICSIALSNGSYGSRLTGAGWGGCTVHLVPGGPNGNIEKVKEALANEFYKVKYPKITDAELENAIIVSKPALGSCLYEL 528
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...--..hhhhhhhhhhhhhhhhhhhh....eeeeeeeeeeee...hhhhh...eeeeeeeeeeeeeee......eeeeee.......eeee...............hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee........hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhhh....eeeee.....eeeee........eeeeeeee.............hhhhhhhhhhhhhhhhhhhhh....--------...hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh-----hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh....eeee.......eeeeeeee....hhhhhhhhhhhhhhhhhh...hhhhhhhheee.......eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------GALACTOKINAS--------------------------------------------------------------------------------------------------GHMP_KINASES------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:9-528 (gaps) UniProt: 1-528 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                Transcript 1
                 2aj4 B   9 VIVPEFNSS--ELPRPLAEKCPSIIKKFISAYDAKPDFVARSPGRVNLIGEHIDYCDFSVLPLAIDFDMLCAVKVLNEKNPSITLINADPKFAQRKFDLPLDGSYVTIDPSVSDWSNYFKCGLHVAHSFLKKLAPERFASAPLAGLQVFCEGDVPTGSGLSSSAAFICAVALAVVKANMGPGYHMSKQNLMRITVVAEHYVGVNNGGMDQAASVCGEEDHALYVEFKPQLKATPFKFPQLKNHEISFVIANTLVVSNKFETAPTNYNLRVVEVTTAANVLAATYGVVLL--------NKGNLRDFMNVYYARYHNISTPWNGDIESGIERLTKMLVLVEESLANKKQGFSVDDVAQSLNCSREEFTRDYLTTSPVRFQVLKLYQRAKHVYSESLRVLKAVKLMTT-----DEDFFKQFGALMNESQASCDKLYECSCPEIDKICSIALSNGSYGSRLTGAGWGGCTVHLVPGGPNGNIEKVKEALANEFYKVKYPKITDAELENAIIVSKPALGSCLYEL 528
                                    |- |      28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288        |-       308       318       328       338       348       358       368       378       388       398       408    |    -|      428       438       448       458       468       478       488       498       508       518       528
                                   17 20                                                                                                                                                                                                                                                                                  297      306                                                                                                        413   419

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 2AJ4)

(no "CATH Domain" information available for 2AJ4)

(no "Pfam Domain" information available for 2AJ4)

Asymmetric Unit(hide GO term definitions)

Chain A,B (GAL1_YEAST | P04385)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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:0033499	galactose catabolic process via UDP-galactose	The chemical reactions and pathways resulting in the breakdown of galactose, via the intermediate UDP-galactose.
	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.
	GO:0000411	positive regulation of transcription by galactose	Any process involving galactose that activates or increases the rate of transcription.
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 (4, 8)

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