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Title :   CRYSTAL STRUCTURE OF E.COLI DHA KINASE DHAK

Authors :   R. Shi, L. Mcdonald, A. Matte, M. Cygler, I. Ekiel, Montreal-Kingston Structural Genomics Initiative (Bsgi)

Date :   19 Nov 10 (Deposition) - 12 Jan 11 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.21

Chains :   Asym./Biol. Unit : A,B

Keywords :   Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Shi, L. Mcdonald, Q. Cui, A. Matte, M. Cygler, I. Ekiel
Structural And Mechanistic Insight Into Covalent Substrate Binding By Escherichia Coli Dihydroxyacetone Kinase.
Proc. Natl. Acad. Sci. Usa V. 108 1302 2011
PubMed-ID: 21209328 | Reference-DOI: 10.1073/PNAS.1012596108

Molecule 1 - PTS-DEPENDENT DIHYDROXYACETONE KINASE, DIHYDROXYACETONE- BINDING SUBUNIT DHAK
	Chains	:	A, B
	EC Number	:	2.7.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	B1200, DHAK, JW5187, YCGT
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K-12

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:52 , GLY A:53 , HIS A:56 , PHE A:78 , SER A:80 , LYS A:104 , ASP A:109 , HIS A:218 , HOH A:420	BINDING SITE FOR RESIDUE GOL A 1228
2	AC2	SOFTWARE	GLY B:52 , GLY B:53 , HIS B:56 , PHE B:78 , LYS B:104 , ASP B:109 , HIS B:218 , HOH B:419	BINDING SITE FOR RESIDUE GOL B 1228

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

Asymmetric/Biological Unit

No.	Residues
1	Asp A:31	-	Pro A:32
2	Ala A:40	-	Pro A:41
3	Glu A:57	-	Pro A:58
4	Met A:59	-	His A:60
5	Tyr A:143	-	Thr A:144
6	Asp B:31	-	Pro B:32
7	Ala B:40	-	Pro B:41
8	Glu B:57	-	Pro B:58
9	Met B:59	-	His B:60

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHAK	PS51481	DhaK domain profile.	DHAK_ECOLI	7-352	2	A:7-352 B:7-352

(no "Exon" information available for 3PNK)

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 A from PDB  Type:PROTEIN  Length:354
 aligned with DHAK_ECOLI | P76015 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:354
                                    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    
           DHAK_ECOLI     2 KKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWG 355
               SCOP domains d3pnka_ A: automated matches                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh..eeee....eeee.........eeeeeeee.....hhhhh......eeeeeee....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh...eeeeee..................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eeeeeeeee.................eeee..........eeee..hhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeee........eeeeeeeeeehhhhhhhhhh.ee....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----DHAK  PDB: A:7-352 UniProt: 7-352                                                                                                                                                                                                                                                                                                                         --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pnk A   2 KKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWG 355
                                    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

Chain B from PDB  Type:PROTEIN  Length:354
 aligned with DHAK_ECOLI | P76015 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:354
                                    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    
           DHAK_ECOLI     2 KKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWG 355
               SCOP domains d3pnkb_ B: automated matches                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------Dak1-3pnkB01 B:16-355                                                                                                                                                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) --------------Dak1-3pnkB02 B:16-355                                                                                                                                                                                                                                                                                                                                Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhhhhhhhh..eeee....eeee.........eeeeeeee.....hhhhh......eeeeeee....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh...eeeeee..................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eeeeeeeee.................eeee..........eeee..hhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeeeeee........eeeeeeeeeehhhhhhhhhh.ee....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----DHAK  PDB: B:7-352 UniProt: 7-352                                                                                                                                                                                                                                                                                                                         --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pnk B   2 KKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWG 355
                                    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

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: DAK1/DegV-like (26)

Superfamily: DAK1/DegV-like (26)

Family: DAK1 (12)

Protein domain: automated matches (6)

Escherichia coli K-12 [TaxId: 83333] (6)

1a	d3pnka_	A:
1b	d3pnkb_	B:

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EDD (22)

Family: Dak1 (10)

Escherichia coli (strain K12) (8)

1a	Dak1-3pnkB01	B:16-355
1b	Dak1-3pnkB02	B:16-355

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DHAK_ECOLI | P76015)

molecular function
	GO:0004371	glycerone kinase activity	Catalysis of the reaction: ATP + glycerone = ADP + glycerone phosphate + 2 H(+).
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0047324	phosphoenolpyruvate-glycerone phosphotransferase activity	Catalysis of the reaction: glycerone + phosphoenolpyruvate = glycerone phosphate + pyruvate.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	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:0042182	ketone catabolic process	The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
	GO:0046365	monosaccharide catabolic process	The chemical reactions and pathways resulting in the breakdown of monosaccharides, polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:40 - Pro A:41	[ RasMol ]
		Ala B:40 - Pro B:41	[ RasMol ]
		Asp A:31 - Pro A:32	[ RasMol ]
		Asp B:31 - Pro B:32	[ RasMol ]
		Glu A:57 - Pro A:58	[ RasMol ]
		Glu B:57 - Pro B:58	[ RasMol ]
		Met A:59 - His A:60	[ RasMol ]
		Met B:59 - His B:60	[ RasMol ]
		Tyr A:143 - Thr A:144	[ RasMol ]

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	3pnk
		Family and Domain Information	:	ProDom \| SYSTERS
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	DHAK_ECOLI \| P76015
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	2.7.-.-
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	DHAK_ECOLI \| P76015
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UniProtKB/Swiss-Prot
	DHAK_ECOLI \| P76015	:	1oi2 1oi3 1uod 1uoe 3pnl 3pnm 3pno 3pnq 4lrx 4lry

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

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