1V1B - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND ATP

Authors :   T. H. Tahirov, E. Inagaki

Date :   13 Apr 04 (Deposition) - 14 Apr 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   2-Keto-3-Deoxygluconate Kinase, Atp, Thermus Thermophilus, Structural Genomics, Transferase, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Ohshima, E. Inagaki, K. Yasuike, K. Takio, T. H. Tahirov
Structure Of Thermus Thermophilus 2-Keto-3-Deoxygluconate Kinase: Evidence For Recognition Of An Open Chain Substrate
J. Mol. Biol. V. 340 477 2004
PubMed-ID: 15210349 | Reference-DOI: 10.1016/J.JMB.2004.04.074
(for further references see the PDB file header)

Molecule 1 - 2-KETO-3-DEOXYGLUCONATE KINASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	ATP	4	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	ATP	6	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	ATP	6	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:165 , SER A:193 , LYS A:219 , GLY A:221 , GLY A:224 , ALA A:238 , PHE A:239 , VAL A:241 , PRO A:246 , GLY A:248 , ALA A:249 , GLY A:250 , ASP A:251 , PHE A:253 , ASN A:275 , ALA A:279	BINDING SITE FOR RESIDUE ATP A1301
2	AC2	SOFTWARE	LYS B:219 , GLY B:221 , GLY B:224 , ALA B:238 , PHE B:239 , VAL B:241 , PRO B:246 , GLY B:248 , ALA B:249 , GLY B:250 , ASP B:251 , PHE B:253 , ASN B:275 , ALA B:279 , HOH B:2030	BINDING SITE FOR RESIDUE ATP B1301
3	AC3	SOFTWARE	SER C:193 , LYS C:219 , GLY C:221 , GLY C:224 , ALA C:238 , PHE C:239 , VAL C:241 , PRO C:246 , GLY C:248 , ALA C:249 , GLY C:250 , ASP C:251 , PHE C:253 , ASN C:275 , ALA C:279	BINDING SITE FOR RESIDUE ATP C1301
4	AC4	SOFTWARE	LYS D:219 , GLY D:221 , GLY D:224 , ALA D:238 , PHE D:239 , VAL D:241 , PRO D:246 , GLY D:248 , ALA D:249 , GLY D:250 , ASP D:251 , PHE D:253 , ASN D:275 , ALA D:279 , HOH D:2018 , HOH D:2019	BINDING SITE FOR RESIDUE ATP D1301

(no "SS Bond" information available for 1V1B)

(no "Cis Peptide Bond" information available for 1V1B)

(no "SAP(SNP)/Variant" information available for 1V1B)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	KDGK_THET8	245-258	4	A:245-258 B:245-258 C:245-258 D:245-258

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	KDGK_THET8	245-258	6	A:245-258 B:245-258 - -

Biological Unit 2 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	KDGK_THET8	245-258	6	- - C:245-258 D:245-258

(no "Exon" information available for 1V1B)

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:301
 aligned with KDGK_THET8 | Q53W83 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:301
                                    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 
           KDGK_THET8     1 MLEVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFGRVEEALRALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLL 301
               SCOP domains d1v1ba_ A: 2-keto-3-deoxygluconate kinase                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1v1bA00 A:1-301  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeeee....hhhhh.eeeeeeehhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhh......eee......eee...........eee...hhhhh......hhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhh...eeeee.....eeee....eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v1b A   1 MLEVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFGRVEEALRALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLL 301
                                    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

Chain B from PDB  Type:PROTEIN  Length:301
 aligned with KDGK_THET8 | Q53W83 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:301
                                    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 
           KDGK_THET8     1 MLEVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFGRVEEALRALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLL 301
               SCOP domains d1v1bb_ B: 2-keto-3-deoxygluconate kinase                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1v1bB00 B:1-301  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeeee....hhhhh.eeeeeeehhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhh......eee......eee...........eee...hhhhhh.....hhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhh...eeeee.....eeee....eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v1b B   1 MLEVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFGRVEEALRALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLL 301
                                    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

Chain C from PDB  Type:PROTEIN  Length:301
 aligned with KDGK_THET8 | Q53W83 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:301
                                    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 
           KDGK_THET8     1 MLEVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFGRVEEALRALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLL 301
               SCOP domains d1v1bc_ C: 2-keto-3-deoxygluconate kinase                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1v1bC00 C:1-301  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeeee....hhhhh.eeeeeeehhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhh......eee......eee...........eee...hhhhhh.....hhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhh...eeeee.....eeee....eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v1b C   1 MLEVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFGRVEEALRALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLL 301
                                    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

Chain D from PDB  Type:PROTEIN  Length:301
 aligned with KDGK_THET8 | Q53W83 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:301
                                    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 
           KDGK_THET8     1 MLEVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFGRVEEALRALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLL 301
               SCOP domains d1v1bd_ D: 2-keto-3-deoxygluconate kinase                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1v1bD00 D:1-301  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeeee....hhhhh.eeeeeeehhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhh......eee......eee...........eee...hhhhhh.....hhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhh...eeeee.....eeee....eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v1b D   1 MLEVVTAGEPLVALVPQEPGHLRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFGRVEEALRALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLL 301
                                    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

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: Ribokinase-like (226)

Superfamily: Ribokinase-like (189)

Family: Ribokinase-like (36)

Protein domain: 2-keto-3-deoxygluconate kinase (5)

Thermus thermophilus [TaxId: 274] (4)

1a	d1v1ba_	A:
1b	d1v1bb_	B:
1c	d1v1bc_	C:
1d	d1v1bd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (109)

Homologous Superfamily: [code=3.40.1190.20, no name defined] (73)

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. (4)

1a	1v1bA00	A:1-301
1b	1v1bB00	B:1-301
1c	1v1bC00	C:1-301
1d	1v1bD00	D:1-301

(no "Pfam Domain" information available for 1V1B)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (KDGK_THET8 | Q53W83)

molecular function
	GO:0008673	2-dehydro-3-deoxygluconokinase activity	Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate + ATP = 2-dehydro-3-deoxy-6-phospho-D-gluconate + ADP + 2 H(+).
	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: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:0004747	ribokinase activity	Catalysis of the reaction: ATP + D-ribose = ADP + D-ribose 5-phosphate.
	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:0006014	D-ribose metabolic process	The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose group of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.
	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: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.

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	KDGK_THET8 \| Q53W83	:	1v19 1v1a 1v1s

1j5v	CRYSTAL STRUCTURE OF 2-KETO-3-DEOXYGLUCONATE KINASE (TM0067)FROM THERMOTOGA MARITIMA AT 2.3 A RESOLUTION
1v19	2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS
1v1a	2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3- DEOXYGLUCONATE AND ADP

Description

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Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

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Cis Peptide Bonds (0, 0)

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