3D1R - JenaLib

Title :   STRUCTURE OF E. COLI GLPX WITH ITS SUBSTRATE FRUCTOSE 1,6-BISPHOSPHATE

Authors :   A. Singer, T. Skarina, A. Dong, G. Brown, A. Joachimiak, A. M. Edwards, A. F. Yakunin, A. Savchenko, Midwest Center For Structural Genom (Mcsg)

Date :   06 May 08 (Deposition) - 23 Dec 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym./Biol. Unit : A

Keywords :   Fructose-1, 6-Bisphosphatase, 6-Bisphosphate, Carbohydrate Metabolism, Hydrolase, Manganese, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Brown, A. Singer, V. V. Lunin, M. Proudfoot, T. Skarina, R. Flick, S. Kochinyan, R. Sanishvili, A. Joachimiak, A. M. Edwards, A. Savchenko, A. F. Yakunin
Structural And Biochemical Characterization Of The Type Ii Fructose-1, 6-Bisphosphatase Glpx From Escherichia Coli.
J. Biol. Chem. V. 284 3784 2009
PubMed-ID: 19073594 | Reference-DOI: 10.1074/JBC.M808186200

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:88 , GLY A:89 , THR A:90 , ARG A:91 , TYR A:119 , LYS A:164 , ARG A:166 , ASP A:186 , GLY A:187 , ASP A:188 , GLY A:210 , GLU A:213 , MG A:3502 , HOH A:3553 , HOH A:3561 , HOH A:3572 , HOH A:3675 , HOH A:3722 , HOH A:3759 , HOH A:3761 , HOH A:3763 , HOH A:3774 , HOH A:3795 , HOH A:3828	BINDING SITE FOR RESIDUE FBP A3499
2	AC2	SOFTWARE	ASP A:85 , GLU A:88 , GLU A:213 , HOH A:3593 , HOH A:3722 , HOH A:3828	BINDING SITE FOR RESIDUE CA A3500
3	AC3	SOFTWARE	FBP A:3499 , HOH A:3675 , HOH A:3759 , HOH A:3761 , HOH A:3762 , HOH A:3763	BINDING SITE FOR RESIDUE MG A3502
4	AC4	SOFTWARE	PRO A:165 , ARG A:166	BINDING SITE FOR RESIDUE CL A3503
5	AC5	SOFTWARE	ASP A:33 , GLU A:57 , HOH A:3538 , HOH A:3544 , HOH A:3731 , HOH A:3829	BINDING SITE FOR RESIDUE CA A 337
6	AC6	SOFTWARE	LEU A:194 , MET A:197 , SER A:200 , VAL A:202 , HOH A:3730	BINDING SITE FOR RESIDUE MG A3504

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:321
 aligned with GLPX_ECOLI | P0A9C9 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:323
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320   
           GLPX_ECOLI     1 MRRELAIEFSRVTESAALAGYKWLGRGDKNTADGAAVNAMRIMLNQVNIDGTIVIGEGEIDEAPMLYIGEKVGTGRGDAVDIAVDPIEGTRMTAMGQANALAVLAVGDKGCFLNAPDMYMEKLIVGPGAKGTIDLNLPLADNLRNVAAALGKPLSELTVTILAKPRHDAVIAEMQQLGVRVFAIPDGDVAASILTCMPDSEVDVLYGIGGAPEGVVSAAVIRALDGDMNGRLLARHDVKGDNEENRRIGEQELARCKAMGIEAGKVLRLGDMARSDNVIFSATGITKGDLLEGISRKGNIATTETLLIRGKSRTIRRIQSIHY 323
               SCOP domains d3d1ra_ A: automated matches                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3d1rA01 A:1-109,A:277-323 Fructose-1,6-Bisphosphatase, subunit A, domain 1                                   3d1rA02 A:110-276  [code=3.40.190.90, no name defined]                                                                                                                 3d1rA01 A:1-109,A:277-323                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....eeeeee...............ee......eeeeeeeeeehhhhhhh.....eeeeeeee..........eeeeeee.hhhh.......hhhhhhhhhhhhhh.hhhh.eeeee.hhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhh......eeeeeeehhhhhhhhhhhhhh..eeeeeeehhhhhhh..-hhhhhhhhhhhhhhhh......eeehhhhh....eeeeeee..........eee..eeeeeeeeee...-.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d1r A   1 MRRELAIEFSRVTESAALAGYKWLGRGDKNTADGAAVNAMRIMLNQVNIDGTIVIGEGEIAEAPMLYIGEKVGTGRGDAVDIAVDPIEGTRMTAMGQANALAVLAVGDKGCFLNAPDMYMEKLIVGPGAKGTIDLNLPLADNLRNVAAALGKPLSELTVTILAKPRHDAVIAEMQQLGVRVFAIPDGDVAASILTCMPDSEVDVLYGIGGAPEGVVSAAVIRALDGDMNGRLLARHDVKGDN-ENRRIGEQELARCKAMGIEAGKVLRLGDMARSDNVIFSATGITKGDLLEGISRKGNIATTETLLIRGKS-TIRRIQSIHY 323
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 | |   250       260       270       280       290       300       310 | |   320   
                                                                                                                                                                                                                                                                           242 |                                                                 312 |         
                                                                                                                                                                                                                                                                             244                                                                   314

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 (2, 2)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (GLPX_ECOLI | P0A9C9)

molecular function
	GO:0042132	fructose 1,6-bisphosphate 1-phosphatase activity	Catalysis of the reaction: D-fructose 1,6-bisphosphate + H2O = D-fructose 6-phosphate + phosphate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0006094	gluconeogenesis	The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
	GO:0006071	glycerol metabolic process	The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Visualization

Interactive Views

Asymmetric/Biological 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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FBP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Met A:1 - Arg A:2	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3d1r
		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
	GLPX_ECOLI \| P0A9C9
		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)
	3.1.3.11
		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

Description