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Biological Unit 5 (Jmol Viewer)

Title :   STRUCTURE OF A TRANSIENT COMPLEX BETWEEN DHA-KINASE SUBUNITS DHAM AND DHAL FROM LACTOCOCCUS LACTIS

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

Date :   04 Apr 08 (Deposition) - 21 Oct 08 (Release) - 09 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: A,C  (1x)
Biol. Unit 3: B,D  (1x)
Biol. Unit 4: A,D  (1x)
Biol. Unit 5: B,C  (1x)

Keywords :   Transient Protein-Protein Complex Transferase Complex Pts- Dependent Dihydroxyacetone Kinase, Atp-Binding, Glycerol Metabolism, Nucleotide-Binding, Phosphotransferase System (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
(for further references see the PDB file header)

Molecule 1 - PTS-DEPENDENT DIHYDROXYACETONE KINASE, ADP- BINDING SUBUNIT DHAL
	Chains	:	A, B
	EC Number	:	2.7.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMS-DHAKLM
	Expression System Strain	:	CB-DELTA-KLM
	Expression System Vector Type	:	PLASMID
	Gene	:	DHAL
	Organism Common	:	STREPTOCOCCUS LACTIS
	Organism Scientific	:	LACTOCOCCUS LACTIS SUBSP. LACTIS
	Strain	:	IL1403

Molecule 2 - PTS-DEPENDENT DIHYDROXYACETONE KINASE, PHOSPHOTRANSFERASE SUBUNIT DHAM
	Chains	:	C, D
	EC Number	:	2.7.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMS-DHAKLM
	Expression System Strain	:	CB-DELTA-KLM
	Expression System Vector Type	:	PLASMID
	Gene	:	DHAM
	Organism Common	:	STREPTOCOCCUS LACTIS
	Organism Scientific	:	LACTOCOCCUS LACTIS SUBSP. LACTIS
	Synonym	:	PHOSPHOTRANSFERASE ENZYME IIA COMPONENT, PTS SYSTEM EIIA COMPONENT

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:	A		C
Biological Unit 3 (1x)	:		B		D
Biological Unit 4 (1x)	:	A			D
Biological Unit 5 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 28)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	MSE	22	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 24)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	22	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 12)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	11	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (2, 12)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	11	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (2, 12)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	11	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 5 (2, 12)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	11	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:29 , ASP B:34 , ASP B:36	BINDING SITE FOR RESIDUE MG B 1212
2	AC2	SOFTWARE	ASP B:34 , ASP B:36	BINDING SITE FOR RESIDUE MG B 1213
3	AC3	SOFTWARE	ASP A:29 , ASP A:34 , ASP A:36	BINDING SITE FOR RESIDUE MG A 1212
4	AC4	SOFTWARE	ASP A:34 , ASP A:36	BINDING SITE FOR RESIDUE MG A 1213
5	AC5	SOFTWARE	ASP B:29 , ASP B:34 , ASP B:36 , HIS B:37 , ASN B:40 , GLY B:77 , ALA B:78 , SER B:79 , LEU B:82 , GLY B:115 , ALA B:117 , THR B:123 , GLY B:160 , ARG B:161 , ASP B:174 , PRO B:175 , GLY B:176	BINDING SITE FOR RESIDUE ADP B 1211
6	AC6	SOFTWARE	ASP A:29 , ASP A:34 , ASP A:36 , HIS A:37 , ASN A:40 , GLY A:77 , ALA A:78 , SER A:79 , LEU A:82 , GLY A:115 , ALA A:117 , THR A:123 , GLY A:160 , ARG A:161 , ASP A:174 , PRO A:175 , GLY A:176	BINDING SITE FOR RESIDUE ADP A 1211

(no "SS Bond" information available for 3CR3)

(no "Cis Peptide Bond" information available for 3CR3)

(no "SAP(SNP)/Variant" information available for 3CR3)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHAL	PS51480	DhaL domain profile.	DHAL_LACLA	5-189	2	A:5-189 B:5-189

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHAL	PS51480	DhaL domain profile.	DHAL_LACLA	5-189	2	A:5-189 B:5-189

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHAL	PS51480	DhaL domain profile.	DHAL_LACLA	5-189	1	A:5-189 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHAL	PS51480	DhaL domain profile.	DHAL_LACLA	5-189	1	- B:5-189

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHAL	PS51480	DhaL domain profile.	DHAL_LACLA	5-189	1	A:5-189 -

Biological Unit 5 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHAL	PS51480	DhaL domain profile.	DHAL_LACLA	5-189	1	- B:5-189

(no "Exon" information available for 3CR3)

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:192
 aligned with DHAL_LACLA | Q9CIV7 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  
           DHAL_LACLA     1 MLTIDTTIEWLGKFNEKIQENKAYLSELDGPIGDGDHGANMARGMSETMKALEVSNFGNVSEIFKKVAMTLMSKVGGASGPLYGSAFLAMSKTAIETLDTSELIYAGLEAIQKRGKAQVGEKTMVDIWSAFLNDLQTDSASKDNLEKVVKASAGLLATKGRASYLGERSIGHIDPGTQSSAYLFETLLEVVA 192
               SCOP domains d3cr3a1 A:1-192 PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----DHAL  PDB: A:5-189 UniProt: 5-189                                                                                                                                                        --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cr3 A   1 LLTIDTTIEWLGKFNEKIQENKAYLSELDGPIGDGDHGANmARGmSETmKALEVSNFGNVSEIFKKVAmTLmSKVGGASGPLYGSAFLAmSKTAIETLDTSELIYAGLEAIQKRGKAQVGEKTmVDIWSAFLNDLQTDSASKDNLEKVVKASAGLLATKGRASYLGERSIGHIDPGTQSSAYLFETLLEVVA 192
                                    10        20        30        40|   |   50        60        70 |      80        90       100       110       120   |   130       140       150       160       170       180       190  
                                                                   41-MSE   |                  69-MSE               90-MSE                           124-MSE                                                                
                                                                       45-MSE                     72-MSE                                                                                                                    
                                                                           49-MSE

Chain B from PDB  Type:PROTEIN  Length:192
 aligned with DHAL_LACLA | Q9CIV7 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  
           DHAL_LACLA     1 MLTIDTTIEWLGKFNEKIQENKAYLSELDGPIGDGDHGANMARGMSETMKALEVSNFGNVSEIFKKVAMTLMSKVGGASGPLYGSAFLAMSKTAIETLDTSELIYAGLEAIQKRGKAQVGEKTMVDIWSAFLNDLQTDSASKDNLEKVVKASAGLLATKGRASYLGERSIGHIDPGTQSSAYLFETLLEVVA 192
               SCOP domains d3cr3b_ B: PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----DHAL  PDB: B:5-189 UniProt: 5-189                                                                                                                                                        --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cr3 B   1 LLTIDTTIEWLGKFNEKIQENKAYLSELDGPIGDGDHGANmARGmSETmKALEVSNFGNVSEIFKKVAmTLmSKVGGASGPLYGSAFLAmSKTAIETLDTSELIYAGLEAIQKRGKAQVGEKTmVDIWSAFLNDLQTDSASKDNLEKVVKASAGLLATKGRASYLGERSIGHIDPGTQSSAYLFETLLEVVA 192
                                    10        20        30        40|   |   50        60        70 |      80        90       100       110       120   |   130       140       150       160       170       180       190  
                                                                   41-MSE   |                  69-MSE               90-MSE                           124-MSE                                                                
                                                                       45-MSE                     72-MSE                                                                                                                    
                                                                           49-MSE

Chain C from PDB  Type:PROTEIN  Length:121
 aligned with DHAM_LACLA | Q9CIV6 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:121
                                    12        22        32        42        52        62        72        82        92       102       112       122 
           DHAM_LACLA     3 YGIVIVSHSPEIASGLKKLIREVAKNISLTAIGGLENGEIGTSFDRVMNAIEENEADNLLTFFDLGSARMNLDLVSEMTDKELTIFNVPLIEGAYTASALLEAGATFEAIKEQLEKMLIEK 123
               SCOP domains d3cr3c_ C: PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit DhaM                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhh..hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cr3 C   3 YGIVIVSHSPEIASGLKKLIREVAKNISLTAIGGLENGEIGTSFDRVmNAIEENEADNLLTFFDLGSARmNLDLVSEmTDKELTIFNVPLIEGAYTASALLEAGATFEAIKEQLEKmLIEK 123
                                    12        22        32        42       |52        62        72       |82        92       102       112      |122 
                                                                          50-MSE                72-MSE  80-MSE                                119-MSE

Chain D from PDB  Type:PROTEIN  Length:121
 aligned with DHAM_LACLA | Q9CIV6 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:121
                                    12        22        32        42        52        62        72        82        92       102       112       122 
           DHAM_LACLA     3 YGIVIVSHSPEIASGLKKLIREVAKNISLTAIGGLENGEIGTSFDRVMNAIEENEADNLLTFFDLGSARMNLDLVSEMTDKELTIFNVPLIEGAYTASALLEAGATFEAIKEQLEKMLIEK 123
               SCOP domains d3cr3d_ D: PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit DhaM                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhh..hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cr3 D   3 YGIVIVSHSPEIASGLKKLIREVAKNISLTAIGGLENGEIGTSFDRVmNAIEENEADNLLTFFDLGSARmNLDLVSEmTDKELTIFNVPLIEGAYTASALLEAGATFEAIKEQLEKmLIEK 123
                                    12        22        32        42       |52        62        72       |82        92       102       112      |122 
                                                                          50-MSE                72-MSE  80-MSE                                119-MSE

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 "CATH Domain" information available for 3CR3)

(no "Pfam Domain" information available for 3CR3)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DHAL_LACLA | Q9CIV7)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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: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: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.
	GO:0016772	transferase activity, transferring phosphorus-containing groups	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
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.

Chain C,D (DHAM_LACLA | Q9CIV6)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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: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:0009401	phosphoenolpyruvate-dependent sugar phosphotransferase system	The uptake and phosphorylation of specific carbohydrates from the extracellular environment; uptake and phosphorylation are coupled, making the PTS a link between the uptake and metabolism of sugars; phosphoenolpyruvate is the original phosphate donor; phosphoenolpyruvate passes the phosphate via a signal transduction pathway, to enzyme 1 (E1), which in turn passes it on to the histidine protein, HPr; the next step in the system involves sugar-specific membrane-bound complex, enzyme 2 (EII), which transports the sugar into the cell; it includes the sugar permease, which catalyzes the transport reactions; EII is usually divided into three different domains, EIIA, EIIB, and EIIC.
	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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

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	3cr3
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	DHAM_LACLA \| Q9CIV6	:	3ct6

2btd	DHAL E.COLI
2iu4	INVOLED IN THE REGULATION OF DHA OPERON IN L.LACTIS
2iu5	INVOLED IN THE REGULATION OF DHA OPERON IN L.LACTIS
2iu6	INVOLED IN THE REGULATION OF DHA OPERON IN L.LACTIS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 28)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Gene Ontology (11, 18)

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