1UN9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE DIHYDROXYACETONE KINASE FROM C. FREUNDII IN COMPLEX WITH AMP-PNP AND MG2+

Authors :   C. Siebold, I. Arnold, L. F. Garcia-Alles, U. Baumann, B. Erni

Date :   08 Sep 03 (Deposition) - 30 Oct 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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

Keywords :   Kinase, Glycerone Kinase, Dha Kinase, Dihydroxyacetone Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Siebold, I. Arnold, L. F. Garcia-Alles, U. Baumann, B. Erni
Crystal Structure Of The Citrobacter Freundii Dihydroxyacetone Kinase Reveals An Eight-Stranded Alpha-Helical Barrel Atp-Binding Domain
J. Biol. Chem. V. 278 48236 2003
PubMed-ID: 12966101 | Reference-DOI: 10.1074/JBC.M305942200

Molecule 1 - DIHYDROXYACETONE KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.29
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	CITROBACTER FREUNDII
	Organism Taxid	:	546
	Synonym	:	GLYCERONE KINASE, DHA KINASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	2HA	2	Ligand/Ion	DIHYDROXYACETONE
2	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3	MG	4	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:380 , ASP A:385 , ASP A:387 , ANP A:1551	BINDING SITE FOR RESIDUE MG A1552
2	AC2	SOFTWARE	ASP A:385 , ASP A:387 , ANP A:1551	BINDING SITE FOR RESIDUE MG A1553
3	AC3	SOFTWARE	ASP B:380 , ASP B:385 , ASP B:387 , ANP B:1551	BINDING SITE FOR RESIDUE MG B1552
4	AC4	SOFTWARE	ASP B:385 , ASP B:387 , ANP B:1551	BINDING SITE FOR RESIDUE MG B1553
5	AC5	SOFTWARE	ASP A:385 , ASP A:387 , THR A:388 , THR A:391 , GLY A:430 , SER A:431 , SER A:432 , LEU A:435 , GLY A:468 , ALA A:470 , THR A:476 , MET A:477 , ASP A:533 , GLY A:535 , MG A:1552 , MG A:1553	BINDING SITE FOR RESIDUE ANP A1551
6	AC6	SOFTWARE	GLY A:57 , GLY A:58 , HIS A:61 , PHE A:83 , ALA A:84 , LYS A:109 , ASP A:114 , HIS A:220	BINDING SITE FOR RESIDUE 2HA A1554
7	AC7	SOFTWARE	ASP B:380 , ASP B:385 , ASP B:387 , THR B:388 , GLY B:430 , SER B:431 , SER B:432 , LEU B:435 , MET B:464 , GLY B:468 , ALA B:470 , THR B:476 , MET B:477 , ILE B:478 , ASP B:533 , PRO B:534 , GLY B:535 , MG B:1552 , MG B:1553	BINDING SITE FOR RESIDUE ANP B1551
8	AC8	SOFTWARE	GLY B:57 , GLY B:58 , HIS B:61 , PHE B:83 , LYS B:109 , ASP B:114 , HIS B:220	BINDING SITE FOR RESIDUE 2HA B1554

(no "SS Bond" information available for 1UN9)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:64	-	His A:65
2	Gly A:290	-	Pro A:291
3	Ala B:64	-	His B:65
4	Gly B:290	-	Pro B:291

(no "SAP(SNP)/Variant" information available for 1UN9)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHAK	PS51481	DhaK domain profile.	DHAK_CITFR	8-327	2	A:8-327 B:8-327
2	DHAL	PS51480	DhaL domain profile.	DHAK_CITFR	356-548	2	A:356-548 B:356-548

(no "Exon" information available for 1UN9)

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:537
 aligned with DHAK_CITFR | P45510 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:550
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550
           DHAK_CITFR     1 MSQFFFNQRTHLVSDVIDGAIIASPWNNLARLESDPAIRIVVRRDLNKNNVAVISGGGSGHEPAHVGFIGKGMLTAAVCGDVFASPSVDAVLTAIQAVTGEAGCLLIVKNYTGDRLNFGLAAEKARRLGYNVEMLIVGDDISLPDNKHPRGIAGTILVHKIAGYFAERGYNLATVLREAQYAASNTFSLGVALSSCHLPQETDAAPRHHPGHAELGMGIHGEPGASVIDTQNSAQVVNLMVDKLLAALPETGRLAVMINNLGGVSVAEMAIITRELASSPLHSRIDWLIGPASLVTALDMKGFSLTAIVLEESIEKALLTEVETSNWPTPVPPREITCVVSSHASARVEFQPSANALVAGIVELVTATLSDLETHLNALDAKVGDGDTGSTFAAAAREIASLLHRQQLPLNNLATLFALIGERLTVVMGGSSGVLMSIFFTAAGQKLEQGANVVEALNTGLAQMKFYGGADEGDRTMIDALQPALTSLLAQPKNLQAAFDAAQAGAERTCLSSKANAGRASYLSSESLLGNMDPGAQRLAMVFKALAESE 550
               SCOP domains d1un9a4 A:1-335 Dihydroxyacetone kinase                                                                                                                                                                                                                                                                                                        d1un9a1 A:336-550 Citrobacter dihydroxyacetone kinase extra ATP-binding domain                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhh......eeee......eeeee........eeeeeeee.....hhhh.......eeeeeee....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh....eeeeee................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eeeeeeeee..................eee...........ee...hhhhhhhhhhhhhhh.......eeeeeee....hhhhhhhhhhhhhh..hhh.eeeeeeee........eeeeeeeee..hhhhhhhhh.................ee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...-------------....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------DHAK  PDB: A:8-327 UniProt: 8-327                                                                                                                                                                                                                                                                                               ----------------------------DHAL  PDB: A:356-548 UniProt: 356-548                                                                                                                                                            -- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1un9 A   1 ASQFFFNQRTHLVSDVIDGAIIASPWNNLARLESDPAIRIVVRRDLNKNNVAVISGGGSGHEPAHVGFIGKGMLTAAVCGDVFASPSVDAVLTAIQAVTGEAGCLLIVKNYTGDRLNFGLAAEKARRLGYNVEMLIVGDDISLPDNKHPRGIAGTILVHKIAGYFAERGYNLATVLREAQYAASNTFSLGVALSSCHLPQETDAAPRHHPGHAELGMGIHGEPGASVIDTQNSAQVVNLMVDKLLAALPETGRLAVMINNLGGVSVAEMAIITRELASSPLHSRIDWLIGPASLVTALDMKGFSLTAIVLEESIEKALLTEVETSNWPTPVPPREITCVVSSHASARVEFQPSANALVAGIVELVTATLSDLETHLNALDAKVGDGDTGSTFAAAAREIASLLHRQQLPLNNLATLFALIGERLTVVMGGSSGVLMSIFFTAAGQKLEQGANVVEALNTGLAQMKFYGGADEGDRTMIDALQPALTSLLAQPKNLQAAFDAAQAGAERTCLSSKA-------------LGNMDPGAQALAMVFKALAESE 550
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510    |    -       530       540       550
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            515           529

Chain B from PDB  Type:PROTEIN  Length:537
 aligned with DHAK_CITFR | P45510 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:550
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550
           DHAK_CITFR     1 MSQFFFNQRTHLVSDVIDGAIIASPWNNLARLESDPAIRIVVRRDLNKNNVAVISGGGSGHEPAHVGFIGKGMLTAAVCGDVFASPSVDAVLTAIQAVTGEAGCLLIVKNYTGDRLNFGLAAEKARRLGYNVEMLIVGDDISLPDNKHPRGIAGTILVHKIAGYFAERGYNLATVLREAQYAASNTFSLGVALSSCHLPQETDAAPRHHPGHAELGMGIHGEPGASVIDTQNSAQVVNLMVDKLLAALPETGRLAVMINNLGGVSVAEMAIITRELASSPLHSRIDWLIGPASLVTALDMKGFSLTAIVLEESIEKALLTEVETSNWPTPVPPREITCVVSSHASARVEFQPSANALVAGIVELVTATLSDLETHLNALDAKVGDGDTGSTFAAAAREIASLLHRQQLPLNNLATLFALIGERLTVVMGGSSGVLMSIFFTAAGQKLEQGANVVEALNTGLAQMKFYGGADEGDRTMIDALQPALTSLLAQPKNLQAAFDAAQAGAERTCLSSKANAGRASYLSSESLLGNMDPGAQRLAMVFKALAESE 550
               SCOP domains d1un9b4 B:1-335 Dihydroxyacetone kinase                                                                                                                                                                                                                                                                                                        d1un9b1 B:336-550 Citrobacter dihydroxyacetone kinase extra ATP-binding domain                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------Dak1-1un9B01 B:22-331                                                                                                                                                                                                                                                                                                 --------------------------------------------------Dak2-1un9B03 B:382-548                                                                                                                                                 -- Pfam domains (1)
           Pfam domains (2) ---------------------Dak1-1un9B02 B:22-331                                                                                                                                                                                                                                                                                                 --------------------------------------------------Dak2-1un9B04 B:382-548                                                                                                                                                 -- Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhhhhhh......eeee......eeeee........eeeeeeee.....hhhh.......eeeeeee....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh....eeeeee................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eeeeeeeee..................eee...........ee...hhhhhhhhhhhhhhh.......eeeeeee....hhhhhhhhhhhhhh..hhh.eeeeeeee........eeeeeeeee..hhhhhhhhh.................ee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...-------------....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------DHAK  PDB: B:8-327 UniProt: 8-327                                                                                                                                                                                                                                                                                               ----------------------------DHAL  PDB: B:356-548 UniProt: 356-548                                                                                                                                                            -- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1un9 B   1 ASQFFFNQRTHLVSDVIDGAIIASPWNNLARLESDPAIRIVVRRDLNKNNVAVISGGGSGHEPAHVGFIGKGMLTAAVCGDVFASPSVDAVLTAIQAVTGEAGCLLIVKNYTGDRLNFGLAAEKARRLGYNVEMLIVGDDISLPDNKHPRGIAGTILVHKIAGYFAERGYNLATVLREAQYAASNTFSLGVALSSCHLPQETDAAPRHHPGHAELGMGIHGEPGASVIDTQNSAQVVNLMVDKLLAALPETGRLAVMINNLGGVSVAEMAIITRELASSPLHSRIDWLIGPASLVTALDMKGFSLTAIVLEESIEKALLTEVETSNWPTPVPPREITCVVSSHASARVEFQPSANALVAGIVELVTATLSDLETHLNALDAKVGDGDTGSTFAAAAREIASLLHRQQLPLNNLATLFALIGERLTVVMGGSSGVLMSIFFTAAGQKLEQGANVVEALNTGLAQMKFYGGADEGDRTMIDALQPALTSLLAQPKNLQAAFDAAQAGAERTCLSSKA-------------LGNMDPGAQALAMVFKALAESE 550
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510    |    -       530       540       550
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            515           529

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: All alpha proteins (14657)

Fold: DhaL-like (6)

Superfamily: DhaL-like (6)

Family: DhaL-like (3)

Protein domain: Citrobacter dihydroxyacetone kinase extra ATP-binding domain (2)

Citrobacter freundii [TaxId: 546] (2)

1a	d1un9a1	A:336-550
1b	d1un9b1	B:336-550

Class: Alpha and beta proteins (a/b) (23833)

Fold: DAK1/DegV-like (26)

Superfamily: DAK1/DegV-like (26)

Family: DAK1 (12)

Protein domain: Dihydroxyacetone kinase (2)

Citrobacter freundii [TaxId: 546] (2)

2a	d1un9a4	A:1-335
2b	d1un9b4	B:1-335

(no "CATH Domain" information available for 1UN9)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EDD (22)

Family: Dak1 (10)

Citrobacter freundii (2)

1a	Dak1-1un9B01	B:22-331
1b	Dak1-1un9B02	B:22-331

Clan: no clan defined [family: Dak2] (3)

Family: Dak2 (3)

Citrobacter freundii (2)

2a	Dak2-1un9B03	B:382-548
2b	Dak2-1un9B04	B:382-548

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DHAK_CITFR | P45510)

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:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0019588	anaerobic glycerol catabolic process	The anaerobic chemical reactions and pathways resulting in the breakdown of glycerol, yielding energy in the form of ATP.
	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/Biological Unit
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	Cis Peptide Bonds
		Ala A:64 - His A:65	[ RasMol ]
		Ala B:64 - His B:65	[ RasMol ]
		Gly A:290 - Pro A:291	[ RasMol ]
		Gly B:290 - Pro B:291	[ RasMol ]

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	2.7.1.29
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	DHAK_CITFR \| P45510	:	1un8

1un8	CRYSTAL STRUCTURE OF THE DIHYDROXYACETONE KINASE OF C. FREUNDII (NATIVE FORM)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

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