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Title :   CRYSTAL STRUCTURE OF 2-DEHYDRO-3- DEOXYGLUCONOKINASE (EC 2.7.1.45) (TM0067) FROM THERMOTOGA MARITIMA AT 2.05 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   25 Jul 05 (Deposition) - 14 Feb 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

Keywords :   Tm0067, 2-Dehydro-3- Deoxygluconokinase, Pfkb Family Carbohydrate Kinase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. I. Mathews, D. Mcmullan, M. D. Miller, J. M. Canaves, M. A. Elsliger, R. Floyd, S. K. Grzechnik, L. Jaroszewski, H. E. Klock, E. Koesema, J. S. Kovarik, A. Kreusch, P. Kuhn, T. M. Mcphillips, A. T. Morse, K. Quijano, C. L. Rife, R. Schwarzenbacher, G. Spraggon, R. C. Stevens H. Van Den Bedem, D. Weekes, G. Wolf, K. O. Hodgson, J. Wooley, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Crystal Structure Of 2-Keto-3-Deoxygluconate Kinase (Tm0067 From Thermotoga Maritima At 2. 05 A Resolution.
Proteins V. 70 603 2007
PubMed-ID: 18004772 | Reference-DOI: 10.1002/PROT.21842

Molecule 1 - 2-KETO-3-DEOXYGLUCONATE KINASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TM0067
	Mutation	:	YES
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	243274
	Strain	:	MSB8

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 24)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	MSE	14	Mod. Amino Acid	SELENOMETHIONINE
3	NI	6	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (1, 42)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MSE	42	Mod. Amino Acid	SELENOMETHIONINE
3	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:67 , HOH A:345 , HOH A:346 , HOH B:345	BINDING SITE FOR RESIDUE NI A 340
02	AC2	SOFTWARE	HIS A:271 , HOH A:347	BINDING SITE FOR RESIDUE NI A 341
03	AC3	SOFTWARE	HIS A:0 , ASP A:48 , HOH A:348 , HOH A:349	BINDING SITE FOR RESIDUE NI A 342
04	AC4	SOFTWARE	ASP A:17 , HOH A:350	BINDING SITE FOR RESIDUE CA A 343
05	AC5	SOFTWARE	HIS A:-3 , HIS A:-4 , GLU A:326 , HOH A:555	BINDING SITE FOR RESIDUE CA A 344
06	AC6	SOFTWARE	HIS B:67 , HOH B:346 , HOH B:347 , HOH B:348	BINDING SITE FOR RESIDUE NI B 340
07	AC7	SOFTWARE	HIS B:271 , HOH B:349	BINDING SITE FOR RESIDUE NI B 341
08	AC8	SOFTWARE	HIS B:263 , HOH B:350 , HOH B:351	BINDING SITE FOR RESIDUE NI B 342
09	AC9	SOFTWARE	ASP B:17	BINDING SITE FOR RESIDUE CA B 343
10	BC1	SOFTWARE	ASP A:25 , HOH A:561 , ASP B:25 , HOH B:368	BINDING SITE FOR RESIDUE CA B 344

(no "SS Bond" information available for 2AFB)

(no "Cis Peptide Bond" information available for 2AFB)

(no "SAP(SNP)/Variant" information available for 2AFB)

(no "PROSITE Motif" information available for 2AFB)

(no "Exon" information available for 2AFB)

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:329
 aligned with Q9WXS2_THEMA | Q9WXS2 from UniProtKB/TrEMBL  Length:339

    Alignment length:336
                                 1                                                                                                                                                                                                                                                                                                                                          
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325      
         Q9WXS2_THEMA     - -----MKVVTFGEIMLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQMGLDAYFVTKLPNNPLGDAAAGHLRKFGVKTDYIARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFDWEKILDGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLWTKEEAQKVMIPFMEYVDVLIANEEDIEKVLGISVEGLDLKTGKLNREAYAKIAEEVTRKYNFKTVGITLRESISATVNYWSVMVFENGQPHFSNRYEIHIVDRVGAGDSFAGALIYGSLMGFDSQKKAEFAAAASCLKHTIPGDFVVLSIEEIEKLASG 331
               SCOP domains d2afba_ A: 2-keto-3-deoxygluconate kinase                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2afbA00 A:-4-331  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee...eeeee.....hhhhh.eeeeeeehhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhh......eee......eeeee........eeeee.........hhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhhhhh.eeeehhhhhhhhhh......-------hhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeee..eeee...eeee.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2afb A  -4 HHHHHmKVVTFGEImLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQmGLDAYFVTKLPNNPLGDAAAGHLRKFGVKTDYIARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFDWEKILDGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLWTKEEAQKVmIPFmEYVDVLIANEEDIEKVLGISVEGL-------NREAYAKIAEEVTRKYNFKTVGITLRESISATVNYWSVmVFENGQPHFSNRYEIHIVDRVGAGDSFAGALIYGSLmGFDSQKKAEFAAAASCLKHTIPGDFVVLSIEEIEKLASG 331
                                 |   5    |   15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175     | 185       195       205   |     - |     225       235       245       255       265       275       285      |295       305       315       325      
                                 1-MSE   10-MSE                             45-MSE                                                                                                                                 181-MSE                     209     217                                   255-MSE                              292-MSE                                   
                                                                                                                                                                                                                       185-MSE

Chain B from PDB  Type:PROTEIN  Length:326
 aligned with Q9WXS2_THEMA | Q9WXS2 from UniProtKB/TrEMBL  Length:339

    Alignment length:332
                             1                                                                                                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329  
         Q9WXS2_THEMA     - -MKVVTFGEIMLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQMGLDAYFVTKLPNNPLGDAAAGHLRKFGVKTDYIARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFDWEKILDGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLWTKEEAQKVMIPFMEYVDVLIANEEDIEKVLGISVEGLDLKTGKLNREAYAKIAEEVTRKYNFKTVGITLRESISATVNYWSVMVFENGQPHFSNRYEIHIVDRVGAGDSFAGALIYGSLMGFDSQKKAEFAAAASCLKHTIPGDFVVLSIEEIEKLASG 331
               SCOP domains d2afbb_ B: 2-keto-3-deoxygluconate kinase                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2afbB00 B:0-331  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeee.....hhhhh.eeeeeeehhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhh......eee......eeeee........eeeee.........hhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhhh...eeeehhhhhhhhhh.......------hhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeee.........eeee.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2afb B   0 HmKVVTFGEImLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQmGLDAYFVTKLPNNPLGDAAAGHLRKFGVKTDYIARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFDWEKILDGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLWTKEEAQKVmIPFmEYVDVLIANEEDIEKVLGISVEGLD------NREAYAKIAEEVTRKYNFKTVGITLRESISATVNYWSVmVFENGQPHFSNRYEIHIVDRVGAGDSFAGALIYGSLmGFDSQKKAEFAAAASCLKHTIPGDFVVLSIEEIEKLASG 331
                             |       9|       19        29        39     |  49        59        69        79        89        99       109       119       129       139       149       159       169       179 |   | 189       199       209|      219       229       239       249     | 259       269       279       289  |    299       309       319       329  
                             1-MSE   10-MSE                             45-MSE                                                                                                                                 181-MSE                      210    217                                   255-MSE                              292-MSE                                   
                                                                                                                                                                                                                   185-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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

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Organisms( (-)

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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)

Thermotoga maritima, TM0067 [TaxId: 2336] (1)

1a	d2afba_	A:
1b	d2afbb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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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)

Thermotoga maritima msb8. Organism_taxid: 243274. Strain: msb8. (3)

1a	2afbB00	B:0-331
1b	2afbA00	A:-4-331

(no "Pfam Domain" information available for 2AFB)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9WXS2_THEMA | Q9WXS2)

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:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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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Description

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Ligands, Modified Residues, Ions (3, 24)

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