1RKS - JenaLib

Title :   E. COLI RIBOKINASE IN COMPLEX WITH D-RIBOSE

Authors :   J. A. Sigrell, A. D. Cameron, S. L. Mowbray

Date :   17 May 99 (Deposition) - 31 Aug 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Carbohydrate Kinase, Ribose, Transferase, Induced Fit (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. Sigrell, A. D. Cameron, S. L. Mowbray
Induced Fit On Sugar Binding Activates Ribokinase.
J. Mol. Biol. V. 290 1009 1999
PubMed-ID: 10438599 | Reference-DOI: 10.1006/JMBI.1999.2938
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:14 , ASP A:16 , GLY A:41 , GLY A:42 , LYS A:43 , ASN A:46 , ALA A:98 , GLU A:143 , ASP A:255 , ALA A:291	BINDING SITE FOR RESIDUE RIB A 311
2	AC2	SOFTWARE	GLY A:28 , THR A:30 , PRO A:169 , ALA A:170 , ASN A:187 , GLU A:190 , HOH A:330	BINDING SITE FOR RESIDUE PO4 A 312
3	AC3	SOFTWARE	HIS A:17 , HOH A:350 , HOH A:363	BINDING SITE FOR RESIDUE PO4 A 313
4	RB1	AUTHOR	ASN A:14 , ASP A:16 , GLY A:42 , LYS A:43 , ASN A:46 , GLU A:143 , ASP A:255	RESIDUES MAKING DIRECT HYDROGEN BONDS WITH RIBOSE.
5	RB2	AUTHOR	ALA A:98 , ILE A:100 , ILE A:110 , ILE A:112 , ILE A:251	RESIDUES WITHIN VAN DER WAALS DISTANCE OF RIBOSE.

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:305
 aligned with RBSK_ECOLI | P0A9J6 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:305
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303     
           RBSK_ECOLI     4 AGSLVVLGSINADHILNLQSFPTPGETVTGNHYQVAFGGKGANQAVAAGRSGANIAFIACTGDDSIGESVRQQLATDNIDITPVSVIKGESTGVALIFVNGEGENVIGIHAGANAALSPALVEAQRERIANASALLMQLESPLESVMAAAKIAHQNKTIVALNPAPARELPDELLALVDIITPNETEAEKLTGIRVENDEDAAKAAQVLHEKGIRTVLITLGSRGVWASVNGEGQRVPGFRVQAVDTIAAGDTFNGALITALLEEKPLPEAIRFAHAAAAIAVTRKGAQPSVPWREEIDAFLDRQ 308
               SCOP domains d1rksa_ A: Ribokinase                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1rksA00 A:4-308  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                                             CATH domains
               Pfam domains PfkB-1rksA01 A:4-298                                                                                                                                                                                                                                                                                   ---------- Pfam domains
         Sec.struct. author ..eeeee.eeeeeeeeee.......eeeeeeeeee....hhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhh.......eeeee....eeeeeeee...eeeeeeee.......hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..eeeee........hhhhhh..eeeeehhhhhhh........hhhhhhhhhhhhh...eeeeee.....eeee..eeeeeee..........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2---------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rks A   4 AGSLVVLGSINADHILNLQSFPTPGETVTGNHYQVAFGGKGANQAVAAGRSGANIAFIACTGDDSIGESVRQQLATDNIDITPVSVIKGESTGVALIFVNGEGENVIGIHAGANAALSPALVEAQRERIANASALLMQLESPLESVMAAAKIAHQNKTIVALNPAPARELPDELLALVDIITPNETEAEKLTGIRVENDEDAAKAAQVLHEKGIRTVLITLGSRGVWASVNGEGQRVPGFRVQAVDTIAAGDTFNGALITALLEEKPLPEAIRFAHAAAAIAVTRKGAQPSVPWREEIDAFLDRQ 308
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (14, 14)

Asymmetric Unit(hide GO term definitions)

Chain A (RBSK_ECOLI | P0A9J6)

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: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: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:0019303	D-ribose catabolic process	The chemical reactions and pathways resulting in the breakdown of D-ribose (ribo-pentose).
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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