3CT4 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF DHA-KINASE SUBUNIT DHAK FROM L. LACTIS

Authors :   J. M. Jeckelmann, A. Zurbriggen, S. Christen, U. Baumann, B. Erni

Date :   11 Apr 08 (Deposition) - 21 Oct 08 (Release) - 08 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (2x)
Biol. Unit 2: B  (2x)
Biol. Unit 3: C  (2x)
Biol. Unit 4: A (2x),B (2x),C (2x)

Keywords :   Pts Dependent, Dihydroxyacetone Kinase Subunit, Tranferase, Covalently Linked 2Ha, Glycerol Metabolism, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Zurbriggen, J. M. Jeckelmann, S. Christen, C. Bieniossek, U. Baumann, B. Erni
X-Ray Structures Of The Three Lactococcus Lactis Dihydroxyacetone Kinase Subunits And Of A Transient Intersubunit Complex.
J. Biol. Chem. V. 283 35789 2008
PubMed-ID: 18957416 | Reference-DOI: 10.1074/JBC.M804893200

Molecule 1 - PTS-DEPENDENT DIHYDROXYACETONE KINASE, DIHYDROXYACETONE- BINDING SUBUNIT DHAK
	Chains	:	A, B, C
	EC Number	:	2.7.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	ROSETTA(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DHAK
	Organism Common	:	STREPTOCOCCUS LACTIS
	Organism Scientific	:	LACTOCOCCUS LACTIS SUBSP. LACTIS
	Organism Taxid	:	1360
	Strain	:	IL 1403

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A
Biological Unit 2 (2x)	:		B
Biological Unit 3 (2x)	:			C
Biological Unit 4 (2x)	:	A (2x)	B (2x)	C (2x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	2HA	3	Ligand/Ion	DIHYDROXYACETONE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	2HA	2	Ligand/Ion	DIHYDROXYACETONE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	2HA	2	Ligand/Ion	DIHYDROXYACETONE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	2HA	2	Ligand/Ion	DIHYDROXYACETONE

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	2HA	-1	Ligand/Ion	DIHYDROXYACETONE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:54 , GLY A:55 , HIS A:58 , PHE A:80 , LYS A:106 , ASP A:111 , HIS A:220	BINDING SITE FOR RESIDUE 2HA A 333
2	AC2	SOFTWARE	GLY B:54 , GLY B:55 , HIS B:58 , PHE B:80 , LYS B:106 , ASP B:111 , HIS B:220	BINDING SITE FOR RESIDUE 2HA B 333
3	AC3	SOFTWARE	GLY C:54 , GLY C:55 , HIS C:58 , PHE C:80 , LYS C:106 , ASP C:111 , HIS C:220	BINDING SITE FOR RESIDUE 2HA C 333

(no "SS Bond" information available for 3CT4)

Asymmetric Unit

No.	Residues
1	Glu A:59	-	Pro A:60
2	Glu B:59	-	Pro B:60
3	Glu C:59	-	Pro C:60

(no "SAP(SNP)/Variant" information available for 3CT4)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHAK	PS51481	DhaK domain profile.	DHAK_LACLA	9-331	3	A:9-331 B:9-331 C:9-331

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHAK	PS51481	DhaK domain profile.	DHAK_LACLA	9-331	2	A:9-331 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHAK	PS51481	DhaK domain profile.	DHAK_LACLA	9-331	2	- B:9-331 -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHAK	PS51481	DhaK domain profile.	DHAK_LACLA	9-331	2	- - C:9-331

Biological Unit 4 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHAK	PS51481	DhaK domain profile.	DHAK_LACLA	9-331	6	A:9-331 B:9-331 C:9-331

(no "Exon" information available for 3CT4)

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:318
 aligned with DHAK_LACLA | Q9CIV8 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:328
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323        
           DHAK_LACLA     4 EKIINQPQDVVSEMLDGLTYAYGDLIEKVPDFEIIQRKSPKSGKVALVSGGGSGHKPAHAGFVGEGMLSAAVCGAIFTSPTPDQIYEAIKSADEGAGVLLIIKNYLGDVMNFEMAREMAEMEEIKVEQIIVDDDIAVENSLYTQGRRGVAGTVLVHKILGAAAHQEASLDEIKDLADKVVKNIKTIGLALSAATVPEVGKPGFVLDDNEIEYGVGIHSEPGYRREKMKTSYELATELVGKLKEEFKFEAGQKYGILVNGMGATPLMEQFIFMNDVAKLLTEENIEILFKKVGNYMTSIDMAGLSLTMIKLEDDQWLKNLNEDVKTISW 331
               SCOP domains d3ct4a_ A: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh..eee.hhhh.eeee........eeeeeeee.....hhhhh......eeeeeee....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh...eeeeee...................hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeeeeee.......----------..eeee..........eeee..hhhhhhhhhhhhhhhhhh.....eeeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeeee.........eeeeeeee..hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----DHAK  PDB: A:9-331 UniProt: 9-331                                                                                                                                                                                                                                                                                                   PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ct4 A   4 EKIINQPQDVVSEMLDGLTYAYGDLIEKVPDFEIIQRKSPKSGKVALVSGGGSGHEPAHAGFVGEGMLSAAVCGAIFTSPTPDQIYEAIKSADEGAGVLLIIKNYLGDVMNFEMAREMAEMEEIKVEQIIVDDDIAVENSLYTQGRRGVAGTVLVHKILGAAAHQEASLDEIKDLADKVVKNIKTIGLALSAATVP----------DNEIEYGVGIHSEPGYRREKMKTSYELATELVGKLKEEFKFEAGQKYGILVNGMGATPLMEQFIFMNDVAKLLTEENIEILFKKVGNYMTSIDMAGLSLTMIKLEDDQWLKNLNEDVKTISW 331
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193     |   -      |213       223       233       243       253       263       273       283       293       303       313       323        
                                                                                                                                                                                                                             199        210

Chain B from PDB  Type:PROTEIN  Length:318
 aligned with DHAK_LACLA | Q9CIV8 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:328
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323        
           DHAK_LACLA     4 EKIINQPQDVVSEMLDGLTYAYGDLIEKVPDFEIIQRKSPKSGKVALVSGGGSGHKPAHAGFVGEGMLSAAVCGAIFTSPTPDQIYEAIKSADEGAGVLLIIKNYLGDVMNFEMAREMAEMEEIKVEQIIVDDDIAVENSLYTQGRRGVAGTVLVHKILGAAAHQEASLDEIKDLADKVVKNIKTIGLALSAATVPEVGKPGFVLDDNEIEYGVGIHSEPGYRREKMKTSYELATELVGKLKEEFKFEAGQKYGILVNGMGATPLMEQFIFMNDVAKLLTEENIEILFKKVGNYMTSIDMAGLSLTMIKLEDDQWLKNLNEDVKTISW 331
               SCOP domains d3ct4b_ B: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh..eee.hhhh.eeee........eeeeeeee.....hhhhh......eeeeeee....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh...eeeeee...................hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeeeeee.......----------..eeee..........eeee..hhhhhhhhhhhhhhhhhh.....eeeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeeee.........eeeeeeee..hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----DHAK  PDB: B:9-331 UniProt: 9-331                                                                                                                                                                                                                                                                                                   PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ct4 B   4 EKIINQPQDVVSEMLDGLTYAYGDLIEKVPDFEIIQRKSPKSGKVALVSGGGSGHEPAHAGFVGEGMLSAAVCGAIFTSPTPDQIYEAIKSADEGAGVLLIIKNYLGDVMNFEMAREMAEMEEIKVEQIIVDDDIAVENSLYTQGRRGVAGTVLVHKILGAAAHQEASLDEIKDLADKVVKNIKTIGLALSAATVP----------DNEIEYGVGIHSEPGYRREKMKTSYELATELVGKLKEEFKFEAGQKYGILVNGMGATPLMEQFIFMNDVAKLLTEENIEILFKKVGNYMTSIDMAGLSLTMIKLEDDQWLKNLNEDVKTISW 331
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193     |   -      |213       223       233       243       253       263       273       283       293       303       313       323        
                                                                                                                                                                                                                             199        210

Chain C from PDB  Type:PROTEIN  Length:318
 aligned with DHAK_LACLA | Q9CIV8 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:328
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323        
           DHAK_LACLA     4 EKIINQPQDVVSEMLDGLTYAYGDLIEKVPDFEIIQRKSPKSGKVALVSGGGSGHKPAHAGFVGEGMLSAAVCGAIFTSPTPDQIYEAIKSADEGAGVLLIIKNYLGDVMNFEMAREMAEMEEIKVEQIIVDDDIAVENSLYTQGRRGVAGTVLVHKILGAAAHQEASLDEIKDLADKVVKNIKTIGLALSAATVPEVGKPGFVLDDNEIEYGVGIHSEPGYRREKMKTSYELATELVGKLKEEFKFEAGQKYGILVNGMGATPLMEQFIFMNDVAKLLTEENIEILFKKVGNYMTSIDMAGLSLTMIKLEDDQWLKNLNEDVKTISW 331
               SCOP domains d3ct4c_ C: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh..eee.hhhh.eeee........eeeeeeee.....hhhhh......eeeeeee....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh...eeeeee...................hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhheeeeeee.......----------..eeee..........eeee..hhhhhhhhhhhhhhhhhh.....eeeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeeee.........eeeeeeee..hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----DHAK  PDB: C:9-331 UniProt: 9-331                                                                                                                                                                                                                                                                                                   PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ct4 C   4 EKIINQPQDVVSEMLDGLTYAYGDLIEKVPDFEIIQRKSPKSGKVALVSGGGSGHEPAHAGFVGEGMLSAAVCGAIFTSPTPDQIYEAIKSADEGAGVLLIIKNYLGDVMNFEMAREMAEMEEIKVEQIIVDDDIAVENSLYTQGRRGVAGTVLVHKILGAAAHQEASLDEIKDLADKVVKNIKTIGLALSAATVP----------DNEIEYGVGIHSEPGYRREKMKTSYELATELVGKLKEEFKFEAGQKYGILVNGMGATPLMEQFIFMNDVAKLLTEENIEILFKKVGNYMTSIDMAGLSLTMIKLEDDQWLKNLNEDVKTISW 331
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193     |   -      |213       223       233       243       253       263       273       283       293       303       313       323        
                                                                                                                                                                                                                             199        210

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: DAK1/DegV-like (26)

Superfamily: DAK1/DegV-like (26)

Family: automated matches (11)

Protein domain: automated matches (11)

Lactococcus lactis [TaxId: 1358] (3)

1a	d3ct4a_	A:
1b	d3ct4b_	B:
1c	d3ct4c_	C:

(no "CATH Domain" information available for 3CT4)

(no "Pfam Domain" information available for 3CT4)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (DHAK_LACLA | Q9CIV8)

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: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: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: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 Unit
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	Cis Peptide Bonds
		Glu A:59 - Pro A:60	[ RasMol ]
		Glu B:59 - Pro B:60	[ RasMol ]
		Glu C:59 - Pro C:60	[ RasMol ]

Biological Units
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	3ct4
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	2.7.-.-
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1uod	DHAK E. COLI
2iu4	INVOLVED IN REGULATION OF DHA OPERON OF L.LACTIS
2iu5	INVOLVED IN REGULATION OF DHA OPERON OF L.LACTIS
2iu6	INVOLVED IN REGULATION OF DHA OPERON OF L.LACTIS

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