3H49 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A PUTATIVE RIBOKINASE (APO FORM) FROM E.COLI AT 1.8A RESOLUTION

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

Date :   18 Apr 09 (Deposition) - 28 Apr 09 (Release) - 28 Apr 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

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

Reference :   L. Satyanarayana, S. Eswaramoorthy, S. K. Burley, S. Swaminathan
Crystal Structure Of A Putative Ribokinase (Apo Form) From E. Coli At 1. 8A Resolution.
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - RIBOKINASE
	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 Type	:	PSGX3 (BC)
	Gene	:	B1772, JW5289, YDJH
	Organism Scientific	:	ESCHERICHIA COLI K-12
	Organism Taxid	:	83333
	Strain	:	K12

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3H49)

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 3H49)

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:255-267

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 2)

	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	1	- B:41-65
2	PFKB_KINASES_2	PS00584	pfkB family of carbohydrate kinases signature 2.	YDJH_ECOLI	254-267	1	- B:255-267

Biological Unit 3 (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:255-267

(no "Exon" information available for 3H49)

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:307
 aligned with YDJH_ECOLI | P77493 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:307
                                    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       
           YDJH_ECOLI     3 NLDVICIGAAIVDIPLQPVSKNIFDVDSYPLERIAMTTGGDAINEATIISRLGHRTALMSRIGKDAAGQFILDHCRKENIDIQSLKQDVSIDTSINVGLVTEDGERTFVTNRNGSLWKLNIDDVDFARFSQAKLLSLASIFNSPLLDGKALTEIFTQAKARQMIICADMIKPRLNETLDDICEALSYVDYLFPNFAEAKLLTGKETLDEIADCFLACGVKTVVIKTGKDGCFIKRGDMTMKVPAVAGITAIDTIGAGDNFASGFIAALLEGKNLRECARFANATAAISVLSVGATTGVKNRKLVEQL 309
               SCOP domains d3h49a_ A: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee...hhhhhhh..........eeehhhhhhhhhhhhh..eeeee.eee.hhhhhhhhhhhhhhh......eee......eeeeee.....eeee....hhhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhh...eee.hhhhhhhhhh..hhhhhhhhhhh....eeeee.....eeeee..eeeee............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------PFKB_KINASES_1           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h49 A   3 NLDVICIGAAIVDIPLQPVSKNIFDVDSYPLERIAmTTGGDAINEATIISRLGHRTALmSRIGKDAAGQFILDHCRKENIDIQSLKQDVSIDTSINVGLVTEDGERTFVTNRNGSLWKLNIDDVDFARFSQAKLLSLASIFNSPLLDGKALTEIFTQAKARQmIICADmIKPRLNETLDDICEALSYVDYLFPNFAEAKLLTGKETLDEIADCFLACGVKTVVIKTGKDGCFIKRGDmTmKVPAVAGITAIDTIGAGDNFASGFIAALLEGKNLRECARFANATAAISVLSVGATTGVKNRKLVEQL 309
                                    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       
                                                              38-MSE                 61-MSE                                                                                                 165-MSE |                                                                  240-MSE                                                                 
                                                                                                                                                                                                  171-MSE                                                                242-MSE

Chain B from PDB  Type:PROTEIN  Length:299
 aligned with YDJH_ECOLI | P77493 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:307
                                    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       
           YDJH_ECOLI     4 LDVICIGAAIVDIPLQPVSKNIFDVDSYPLERIAMTTGGDAINEATIISRLGHRTALMSRIGKDAAGQFILDHCRKENIDIQSLKQDVSIDTSINVGLVTEDGERTFVTNRNGSLWKLNIDDVDFARFSQAKLLSLASIFNSPLLDGKALTEIFTQAKARQMIICADMIKPRLNETLDDICEALSYVDYLFPNFAEAKLLTGKETLDEIADCFLACGVKTVVIKTGKDGCFIKRGDMTMKVPAVAGITAIDTIGAGDNFASGFIAALLEGKNLRECARFANATAAISVLSVGATTGVKNRKLVEQLL 310
               SCOP domains d3h49b_ B: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeee...hhhhhh...........eeehhhhhhhhhhhhh...eeee.eee.hhhhhhhhhhhhhhh......eee......eeeeee.....eeee....hhhhh.hhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhh...eee.hhhhhhhhhh..hhhhhhhhhhh....eeeee.....eeeee..eeeee..--------..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PFKB_KINASES_1           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h49 B   4 LDVICIGAAIVDIPLQPVSKNIFDVDSYPLERIAmTTGGDAINEATIISRLGHRTALmSRIGKDAAGQFILDHCRKENIDIQSLKQDVSIDTSINVGLVTEDGERTFVTNRNGSLWKLNIDDVDFARFSQAKLLSLASIFNSPLLDGKALTEIFTQAKARQmIICADmIKPRLNETLDDICEALSYVDYLFPNFAEAKLLTGKETLDEIADCFLACGVKTVVIKTGKDGCFIKRGDmTmKVPA--------TIGAGDNFASGFIAALLEGKNLRECARFANATAAISVLSVGATTGVKNRKLVEQLL 310
                                    13        23        33    |   43        53       |63        73        83        93       103       113       123       133       143       153       163 |     173       183       193       203       213       223       233      |243  |      - |     263       273       283       293       303       
                                                             38-MSE                 61-MSE                                                                                                 165-MSE |                                                                  240-MSE46      255                                                       
                                                                                                                                                                                                 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	d3h49a_	A:
1b	d3h49b_	B:

(no "CATH Domain" information available for 3H49)

(no "Pfam Domain" information available for 3H49)

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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 3h49)

	Cis Peptide Bonds
		Gln A:19 - Pro A:20	[ RasMol ]
		Gln B:19 - Pro B:20	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3h49
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	YDJH_ECOLI \| P77493
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.1.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	YDJH_ECOLI \| P77493
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	YDJH_ECOLI \| P77493	:	3in1

(no "Related Entries Specified in the PDB File" available for 3H49)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 12)

Sites (0, 0)

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

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File