2C49 - JenaLib

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Title :   CRYSTAL STRUCTURE OF METHANOCALDOCOCCUS JANNASCHII NUCLEOSIDE KINASE - AN ARCHAEAL MEMBER OF THE RIBOKINASE FAMILY

Authors :   L. Arnfors, T. Hansen, W. Meining, P. Schoenheit, R. Ladenstein

Date :   17 Oct 05 (Deposition) - 30 Aug 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.92

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

Keywords :   Transferase, Nucleoside Kinase, Hyperthermophile, Ribokinase Family, Ribokinase Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Arnfors, T. Hansen, P. Schoenheit, R. Ladenstein, W. Meining
Structure Of Methanocaldococcus Jannaschii Nucleoside Kinase: An Archaeal Member Of The Ribokinase Family.
Acta Crystallogr. , Sect. D V. 62 1085 2006
PubMed-ID: 16929110 | Reference-DOI: 10.1107/S0907444906024826

Molecule 1 - SUGAR KINASE MJ0406
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET17B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	METHANOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Other Details	:	METHANOCALDOCOCCUS JANNASCHII
	Synonym	:	NUCLEOSIDE 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	ADN	2	Ligand/Ion	ADENOSINE
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	HOH A:2046 , HOH A:2056 , HOH A:2057 , HOH A:2066 , HOH A:2077 , HOH A:2079	BINDING SITE FOR RESIDUE MG A1302
2	AC2	SOFTWARE	HOH A:2018 , HOH A:2019 , HOH A:2021 , HOH A:2042 , HOH A:2054	BINDING SITE FOR RESIDUE MG A1303
3	AC3	SOFTWARE	HOH B:2014 , HOH B:2040 , HOH B:2041 , HOH B:2053 , HOH B:2081 , HOH B:2082	BINDING SITE FOR RESIDUE MG B1302
4	AC4	SOFTWARE	HOH B:2036 , HOH B:2048 , HOH B:2058 , HOH B:2059 , HOH B:2078	BINDING SITE FOR RESIDUE MG B1303
5	AC5	SOFTWARE	HIS A:13 , ALA A:15 , ASP A:17 , GLY A:42 , GLY A:43 , ASN A:47 , THR A:111 , PHE A:113 , GLN A:163 , ASP A:164 , ASP A:247 , CYS A:283 , HOH A:2077 , HOH A:2078 , SER B:31 , GLN B:33	BINDING SITE FOR RESIDUE ADN A1301
6	AC6	SOFTWARE	GLN A:109 , ASN A:186 , THR A:214 , GLY A:216 , GLY A:219 , CYS A:233 , ILE A:234 , VAL A:239 , THR A:243 , ALA A:245 , GLY A:246 , ALA A:274 , HOH A:2062 , HOH A:2072 , HOH A:2079 , HOH A:2080	BINDING SITE FOR RESIDUE ANP A1304
7	AC7	SOFTWARE	HIS B:13 , ALA B:15 , ASP B:17 , GLY B:42 , GLY B:43 , ALA B:44 , HOH B:2080	BINDING SITE FOR RESIDUE ADN B1301
8	AC8	SOFTWARE	ASN B:186 , THR B:214 , LYS B:215 , GLY B:216 , GLY B:219 , CYS B:233 , ILE B:234 , VAL B:239 , PRO B:242 , THR B:243 , GLY B:244 , ALA B:245 , GLY B:246 , TYR B:249 , ARG B:250 , ALA B:274 , HOH B:2060 , HOH B:2081 , HOH B:2082	BINDING SITE FOR RESIDUE ANP B1304

(no "SS Bond" information available for 2C49)

(no "Cis Peptide Bond" information available for 2C49)

(no "SAP(SNP)/Variant" information available for 2C49)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFKB_KINASES_1	PS00583	pfkB family of carbohydrate kinases signature 1.	NK_METJA	42-66	2	A:42-66 B:42-66
2	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	NK_METJA	241-254	2	A:241-254 B:241-254

(no "Exon" information available for 2C49)

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:299
 aligned with NK_METJA | Q57849 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:299
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292         
             NK_METJA     3 GKMEKITCVGHTALDYIFNVEKFPEPNTSIQIPSARKYYGGAAANTAVGIKKLGVNSELLSCVGYDFKNSGYERYLKNLDINISKLYYSEEEETPKAWIFTDKDNNQITFFLWGAAKHYKELNPPNFNTEIVHIATGDPEFNLKCAKKAYGNNLVSFDPGQDLPQYSKEMLLEIIEHTNFLFMNKHEFERASNLLNFEIDDYLERVDALIVTKGSKGSVIYTKDKKIEIPCIKAGKVIDPTGAGDSYRAGFLSAYVKGYDLEKCGLIGAATASFVVEAKGCQTNLPTWDKVVERLEKHR 301
               SCOP domains d2c49a_ A: automated matches                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeeeeee........eeeee....eeeehhhhhhhhhhhhh..eeeee.ee......hhhhhhhhhh.......ee.......eeeeee.....eeeeee.hhhhhhhhh......eeeeeee..hhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhh.hhhhhhh...eeeee.hhh.eeee....eeee............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------PFKB_KINASES_1           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c49 A   3 GKMEKITCVGHTALDYIFNVEKFPEPNTSIQIPSARKYYGGAAANTAVGIKKLGVNSELLSCVGYDFKNSGYERYLKNLDINISKLYYSEEEETPKAWIFTDKDNNQITFFLWGAAKHYKELNPPNFNTEIVHIATGDPEFNLKCAKKAYGNNLVSFDPGQDLPQYSKEMLLEIIEHTNFLFMNKHEFERASNLLNFEIDDYLERVDALIVTKGSKGSVIYTKDKKIEIPCIKAGKVIDPTGAGDSYRAGFLSAYVKGYDLEKCGLIGAATASFVVEAKGCQTNLPTWDKVVERLEKHR 301
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292

Chain B from PDB  Type:PROTEIN  Length:298
 aligned with NK_METJA | Q57849 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:298
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292        
             NK_METJA     3 GKMEKITCVGHTALDYIFNVEKFPEPNTSIQIPSARKYYGGAAANTAVGIKKLGVNSELLSCVGYDFKNSGYERYLKNLDINISKLYYSEEEETPKAWIFTDKDNNQITFFLWGAAKHYKELNPPNFNTEIVHIATGDPEFNLKCAKKAYGNNLVSFDPGQDLPQYSKEMLLEIIEHTNFLFMNKHEFERASNLLNFEIDDYLERVDALIVTKGSKGSVIYTKDKKIEIPCIKAGKVIDPTGAGDSYRAGFLSAYVKGYDLEKCGLIGAATASFVVEAKGCQTNLPTWDKVVERLEKH 300
               SCOP domains d2c49b_ B: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeeeeee.........eeee...eeeeehhhhhhhhhhhhh..eeeee.ee......hhhhhhhhhh.......ee.......eeeeee.....eeeeee.hhhhhhhhh......eeeeee...hhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh.hhhhhhh...eeeee.hhh.eeee....eeee............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------PFKB_KINASES_1           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c49 B   3 GKMEKITCVGHTALDYIFNVEKFPEPNTSIQIPSARKYYGGAAANTAVGIKKLGVNSELLSCVGYDFKNSGYERYLKNLDINISKLYYSEEEETPKAWIFTDKDNNQITFFLWGAAKHYKELNPPNFNTEIVHIATGDPEFNLKCAKKAYGNNLVSFDPGQDLPQYSKEMLLEIIEHTNFLFMNKHEFERASNLLNFEIDDYLERVDALIVTKGSKGSVIYTKDKKIEIPCIKAGKVIDPTGAGDSYRAGFLSAYVKGYDLEKCGLIGAATASFVVEAKGCQTNLPTWDKVVERLEKH 300
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292

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

Fold: Ribokinase-like (226)

Superfamily: Ribokinase-like (189)

Family: automated matches (88)

Protein domain: automated matches (88)

Methanococcus jannaschii [TaxId: 2190] (2)

1a	d2c49a_	A:
1b	d2c49b_	B:

(no "CATH Domain" information available for 2C49)

(no "Pfam Domain" information available for 2C49)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NK_METJA | Q57849)

molecular function
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2c49)

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	NK_METJA \| Q57849	:	2c4e

2c4e	CRYSTAL STRUCTURE OF METHANOCALDOCOCCUS JANNASCHII NUCLEOSIDE KINASE - AN ARCHAEAL MEMBER OF THE RIBOKINASE FAMILY

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (7, 7)

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