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Title :   CRYSTAL STRUCTURE OF A PUTATIVE RIBOKINASE IN COMPLEX WITH ADP FROM E.COLI

Authors :   L. Satyanarayana, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   11 Aug 09 (Deposition) - 08 Sep 09 (Release) - 08 Sep 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Ribokinase, Transferase, Pfkb Family, Sugar Kinase Ydjh, Adp Nysgxrc, 11206A, Psi2, Kinase, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Satyanarayana, S. K. Burley, S. Swaminathan
Crystal Structure Of A Putative Ribokinase In Complex With Adp From E. Coli
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - UNCHARACTERIZED SUGAR KINASE YDJH
	Chains	:	A, B
	EC Number	:	2.7.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSGX3
	Expression System Strain	:	BL21(DE3)CODON+RIL
	Expression System Taxid	:	562
	Expression System Vector	:	BC PSGX3 (BC)
	Expression System Vector Type	:	PLASMID
	Gene	:	B1772, JW5289, YDJH, YDJH/B1772/JW5289
	Organism Scientific	:	ESCHERICHIA COLI K-12
	Organism Taxid	:	83333
	Strain	:	STRAIN K12

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:196 , LYS A:227 , GLY A:229 , LYS A:230 , GLY A:232 , ALA A:246 , THR A:255 , ASN A:284 , ALA A:287 , HOH A:394 , NA A:411 , HOH A:414 , HOH A:417	BINDING SITE FOR RESIDUE ADP A 510
2	AC2	SOFTWARE	THR A:255 , ALA A:258 , GLY A:259 , ADP A:510	BINDING SITE FOR RESIDUE NA A 411
3	AC3	SOFTWARE	ASN B:196 , LYS B:227 , GLY B:229 , GLY B:232 , ALA B:246 , VAL B:247 , ILE B:250 , ALA B:252 , THR B:255 , ASN B:284 , ALA B:287 , HOH B:385 , NA B:411 , HOH B:421	BINDING SITE FOR RESIDUE ADP B 510
4	AC4	SOFTWARE	GLY B:259 , ADP B:510	BINDING SITE FOR RESIDUE NA B 411

Asymmetric Unit

No.	Residues
1	A:184	-	A:219
2	B:184	-	B:219

Asymmetric Unit

No.	Residues
1	Gln A:19	-	Pro A:20
2	Gln B:19	-	Pro B:20

(no "SAP(SNP)/Variant" information available for 3IN1)

Asymmetric 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.	YDJH_ECOLI	41-65	2	A:41-65 B:41-65
2	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	YDJH_ECOLI	254-267	2	A:254-267 B:254-267

Biological Unit 1 (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.	YDJH_ECOLI	41-65	2	A:41-65 B:41-65
2	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	YDJH_ECOLI	254-267	2	A:254-267 B:254-267

Biological Unit 2 (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.	YDJH_ECOLI	41-65	2	A:41-65 B:41-65
2	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	YDJH_ECOLI	254-267	2	A:254-267 B:254-267

(no "Exon" information available for 3IN1)

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:312
 aligned with YDJH_ECOLI | P77493 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:312
                                    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       302       312  
           YDJH_ECOLI     3 NLDVICIGAAIVDIPLQPVSKNIFDVDSYPLERIAMTTGGDAINEATIISRLGHRTALMSRIGKDAAGQFILDHCRKENIDIQSLKQDVSIDTSINVGLVTEDGERTFVTNRNGSLWKLNIDDVDFARFSQAKLLSLASIFNSPLLDGKALTEIFTQAKARQMIICADMIKPRLNETLDDICEALSYVDYLFPNFAEAKLLTGKETLDEIADCFLACGVKTVVIKTGKDGCFIKRGDMTMKVPAVAGITAIDTIGAGDNFASGFIAALLEGKNLRECARFANATAAISVLSVGATTGVKNRKLVEQLLEEYE 314
               SCOP domains d3in1a_ A: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee...eeeeeeeee..hhhhh..........eeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhh.....eeee......eeeeeee....eeee....hhhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhh...eee.hhhhhhhhhh..hhhhhhhhhhhh...eeeee.hhh.eeeee..eeeee............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..........hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------PFKB_KINASES_1           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2----------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3in1 A   3 NLDVICIGAAIVDIPLQPVSKNIFDVDSYPLERIAmTTGGDAINEATIISRLGHRTALmSRIGKDAAGQFILDHCRKENIDIQSLKQDVSIDTSINVGLVTEDGERTFVTNRNGSLWKLNIDDVDFARFSQAKLLSLASIFNSPLLDGKALTEIFTQAKARQmIICADmIKPRLNETLDDICEALSYVDYLFPNFAEAKLLTGKETLDEIADCFLACGVKTVVIKTGKDGCFIKRGDmTmKVPAVAGITAIDTIGAGDNFASGFIAALLEGKNLRECARFANATAAISVLSVGATTGVKNRKLVEQLLEEYE 314
                                    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       302       312  
                                                              38-MSE                 61-MSE                                                                                                 165-MSE |                                                                  240-MSE                                                                      
                                                                                                                                                                                                  171-MSE                                                                242-MSE

Chain B from PDB  Type:PROTEIN  Length:312
 aligned with YDJH_ECOLI | P77493 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:312
                                    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       302       312  
           YDJH_ECOLI     3 NLDVICIGAAIVDIPLQPVSKNIFDVDSYPLERIAMTTGGDAINEATIISRLGHRTALMSRIGKDAAGQFILDHCRKENIDIQSLKQDVSIDTSINVGLVTEDGERTFVTNRNGSLWKLNIDDVDFARFSQAKLLSLASIFNSPLLDGKALTEIFTQAKARQMIICADMIKPRLNETLDDICEALSYVDYLFPNFAEAKLLTGKETLDEIADCFLACGVKTVVIKTGKDGCFIKRGDMTMKVPAVAGITAIDTIGAGDNFASGFIAALLEGKNLRECARFANATAAISVLSVGATTGVKNRKLVEQLLEEYE 314
               SCOP domains d3in1b_ B: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee...eeeeeeeee.................eeehhhhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhhhh.....eeee......eeeeeee....eeee....hhhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhh...eee.hhhhhhhhhh..hhhhhhhhhhhh...eeeee.hhh.eeee....eeee............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------PFKB_KINASES_1           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2----------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3in1 B   3 NLDVICIGAAIVDIPLQPVSKNIFDVDSYPLERIAmTTGGDAINEATIISRLGHRTALmSRIGKDAAGQFILDHCRKENIDIQSLKQDVSIDTSINVGLVTEDGERTFVTNRNGSLWKLNIDDVDFARFSQAKLLSLASIFNSPLLDGKALTEIFTQAKARQmIICADmIKPRLNETLDDICEALSYVDYLFPNFAEAKLLTGKETLDEIADCFLACGVKTVVIKTGKDGCFIKRGDmTmKVPAVAGITAIDTIGAGDNFASGFIAALLEGKNLRECARFANATAAISVLSVGATTGVKNRKLVEQLLEEYE 314
                                    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       302       312  
                                                              38-MSE                 61-MSE                                                                                                 165-MSE |                                                                  240-MSE                                                                      
                                                                                                                                                                                                  171-MSE                                                                242-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(

)

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)

Escherichia coli K-12 [TaxId: 83333] (5)

1a	d3in1a_	A:
1b	d3in1b_	B:

(no "CATH Domain" information available for 3IN1)

(no "Pfam Domain" information available for 3IN1)

Asymmetric Unit(hide GO term definitions)

Chain A,B (YDJH_ECOLI | P77493)

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.

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UniProtKB/Swiss-Prot
	YDJH_ECOLI \| P77493	:	3h49

3h49	CRYSTAL STRUCTURE OF A PUTATIVE RIBOKINASE (APO FORM) FROM E.COLI AT 1.8A RESOLUTION
3hic	THE CRYSTAL STRUCTURE OF PHOSPHOFRUCTOKINASE(LIN2199)FROM LISTERIA INNOCUA
3i3y	CRYSTAL STRUCTURE OF RIBOKINASE IN COMPLEX WITH D-RIBOSE FROM KLEBSIELLA PNEUMONIAE
3ie7	THE CRYSTAL STRUCTURE OF PHOSPHOFRUCTOKINASE (LIN2199) FROM LISTERIA INNOCUA IN COMPLEX WITH ATP AT 1.6A RELATED ID: NYSGXRC-11206A RELATED DB: TARGETDB
3ikh	CRYSTAL STRUCTURE OF RIBOKINASE IN COMPLEX WITH ATP AND GLYCEROL IN THE ACTIVE SITE FROM KLEBSIELLA PNEUMONIAE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Sites (4, 4)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

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Gene Ontology (7, 7)

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