3LM9 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FRUCTOKINASE WITH ADP AND FRUCTOSE BOUND IN THE ACTIVE SITE

Authors :   B. Nocek, A. Stein, M. Cuff, L. Volkart, A. Joachimiak, Midwest Center Structural Genomics (Mcsg)

Date :   29 Jan 10 (Deposition) - 09 Mar 10 (Release) - 10 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   Fructokinase, Adp-Binding, Fructose-Binding, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Atp-Binding, Carbohydrate Metabolism, Kinase, Magnesium, Metal-Binding, Nucleotide-Binding, Polysaccharide Degradation, Transferase, Reductively Methylated (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Nocek, A. J. Stein, R. Jedrzejczak, M. E. Cuff, H. Li, L. Volkart, A. Joachimiak
Structural Studies Of Rok Fructokinase Ydhr From Bacillus Subtilis: Insights Into Substrate Binding And Fructose Specificity.
J. Mol. Biol. V. 406 325 2011
PubMed-ID: 21185308 | Reference-DOI: 10.1016/J.JMB.2010.12.021

Molecule 1 - FRUCTOKINASE
	Chains	:	A
	EC Number	:	2.7.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	GMUE, YDHR, BSU05860
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	GLUCOMANNAN UTILIZATION PROTEIN E

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 12)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	FRU	1	Ligand/Ion	FRUCTOSE
3	MLY	2	Mod. Amino Acid	N-DIMETHYL-LYSINE
4	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	1	Ligand/Ion	SULFATE ION
6	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (5, 22)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	FRU	2	Ligand/Ion	FRUCTOSE
3	MLY	4	Mod. Amino Acid	N-DIMETHYL-LYSINE
4	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
5	SO4	2	Ligand/Ion	SULFATE ION
6	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:59 , ASP A:103 , VAL A:104 , ILE A:132 , GLU A:150 , HIS A:153 , GLU A:176 , TYR A:252 , HOH A:301 , HOH A:380	BINDING SITE FOR RESIDUE FRU A 1001
2	AC2	SOFTWARE	PRO A:77 , LYS A:78 , ALA A:79 , ASN A:274 , HOH A:370 , HOH A:372	BINDING SITE FOR RESIDUE SO4 A 2001
3	AC3	SOFTWARE	GLY A:129 , THR A:130 , GLY A:181 , PRO A:182 , GLU A:185 , ALA A:192 , ALA A:193 , GLY A:229 , GLY A:230 , GLN A:233 , GLN A:234 , HOH A:380	BINDING SITE FOR RESIDUE ADP A 3001
4	AC4	SOFTWARE	HIS A:153 , CYS A:168 , HIS A:171 , CYS A:174	BINDING SITE FOR RESIDUE ZN A 302

(no "SS Bond" information available for 3LM9)

Asymmetric Unit

No.	Residues
1	Gly A:59	-	Pro A:60

(no "SAP(SNP)/Variant" information available for 3LM9)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ROK	PS01125	ROK family signature.	SCRK_BACSU	128-153	1	A:128-153

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ROK	PS01125	ROK family signature.	SCRK_BACSU	128-153	2	A:128-153

(no "Exon" information available for 3LM9)

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:294
 aligned with SCRK_BACSU | O05510 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:294
                             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    
           SCRK_BACSU     - -MLGGIEAGGTKFVCAVGREDGTIIDRIEFPTKMPDETIEKVIQYFSQFSLQAIGIGSFGPVDNDKTSQTYGTITATPKAGWRHYPFLQTVKNEMKIPVGFSTDVNAAALGEFLFGEAKGLDSCLYITIGTGIGAGAIVEGRLLQGLSHPEMGHIYIRRHPDDVYQGKCPYHGDCFEGLASGPAIEARWGKKAADLSDIAQVWELEGYYIAQALAQYILILAPKKIILGGGVMQQKQVFSYIYQYVPKIMNSYLDFSELSDDISDYIVPPRLGSNAGIIGTLVLAHQALQAEAA 293
               SCOP domains d3lm9a1 A:0-118 Putative fructokinase YhdR                                                                             d3lm9a2 A:119-293 Putative fructokinase YhdR                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----ROK-3lm9A01 A:4-184                                                                                                                                                                  ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeeee.....eeeeeeee..hhhhhhhhhhhhhh.....eeeeee...........................hhhhhhhhhhh..eeeeehhhhhhhhhhhhh.......eeeeee...eeeeeee..ee.......hhhhh...................hhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhh....hhhhh.hhhh.ee...hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------ROK  PDB: A:128-153       -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lm9 A   0 AmLGGIEAGGTKFVCAVGREDGTIIDRIEFPTKmPDETIEKVIQYFSQFSLQAIGIGSFGPVDNDKTSQTYGTITATPKAGWRHYPFLQTVKNEmKIPVGFSTDVNAAALGEFLFGEAKGLDSCLYITIGTGIGAGAIVEGRLLQGLSHPEmGHIYIRRHPDDVYQGKCPYHGDCFEGLASGPAIEARWGKKAADLSDIAQVWELEGYYIAQALAQYILILAPkkIILGGGVmQQKQVFSYIYQYVPKImNSYLDFSELSDDISDYIVPPRLGSNAGIIGTLVLAHQALQAEAA 293
                             |       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    
                             |                              33-MSE                                                       94-MSE                                                  151-MSE                                                                 223-MLY  232-MSE          249-MSE                                        
                             1-MSE                                                                                                                                                                                                                        224-MLY

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: Ribonuclease H-like motif (1424)

Superfamily: Actin-like ATPase domain (426)

Family: ROK (11)

Protein domain: Putative fructokinase YhdR (3)

Bacillus subtilis [TaxId: 1423] (3)

1a	d3lm9a1	A:0-118
1b	d3lm9a2	A:119-293

(no "CATH Domain" information available for 3LM9)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Actin_ATPase (173)

Family: ROK (9)

Bacillus subtilis (3)

ROK-3lm9A01

A:4-184

Asymmetric Unit(hide GO term definitions)

Chain A (SCRK_BACSU | O05510)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008865	fructokinase activity	Catalysis of the reaction: ATP + D-fructose = ADP + D-fructose 6-phosphate.
	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: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: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.
	GO:0000272	polysaccharide catabolic process	The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:59 - Pro A:60	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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3epq	RELATED ID: APC1098 RELATED DB: TARGETDB

Description

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Chains, Units

Ligands, Modified Residues, Ions (6, 12)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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