3L8E - JenaLib

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Title :   CRYSTAL STRUCTURE OF APO FORM OF D,D-HEPTOSE 1.7-BISPHOSPHATE PHOSPHATASE FROM E. COLI

Authors :   H. Nguyen, E. Peisach, K. N. Allen

Date :   31 Dec 09 (Deposition) - 02 Feb 10 (Release) - 23 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.64

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

Keywords :   Had Superfamily, Gmhb, D-Glycero-D-Manno-Heptose-1, 7- Bisphosphate Phosphatase, Carbohydrate Metabolism, Cytoplasm, Hydrolase, Lipopolysaccharide Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. H. Nguyen, L. Wang, H. Huang, E. Peisach, D. Dunaway-Mariano, K. N. Allen
Structural Determinants Of Substrate Recognition In The Had Superfamily Member D-Glycero-D-Manno-Heptose-1, 7-Bisphosphate Phosphatase (Gmhb) .
Biochemistry V. 49 1082 2010
PubMed-ID: 20050614 | Reference-DOI: 10.1021/BI902019Q

Molecule 1 - D,D-HEPTOSE 1,7-BISPHOSPHATE PHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.1.3.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3
	Expression System Strain	:	B-834
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	B0200, GMHB, JW0196, YAED
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	D-GLYCERO-D-MANNO-HEPTOSE 1,7-BISPHOSPHATE PHOSPHATASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:92 , HIS A:94 , CYS A:107 , CYS A:109 , ARG A:110	BINDING SITE FOR RESIDUE ZN A 801
2	AC2	SOFTWARE	ASP A:11 , ARG A:12 , ASP A:13 , THR A:53 , ASN A:54 , LYS A:111 , LYS A:137 , HOH A:202	BINDING SITE FOR RESIDUE ACY A 901
3	AC3	SOFTWARE	CYS B:92 , HIS B:94 , CYS B:107 , CYS B:109 , ARG B:110	BINDING SITE FOR RESIDUE ZN B 802
4	AC4	SOFTWARE	ASP B:11 , ARG B:12 , ASP B:13 , THR B:53 , ASN B:54 , LYS B:111 , LYS B:137 , HOH B:193	BINDING SITE FOR RESIDUE ACY B 902

(no "SS Bond" information available for 3L8E)

Asymmetric Unit

No.	Residues
1	Lys A:111	-	Pro A:112
2	Lys B:111	-	Pro B:112

(no "SAP(SNP)/Variant" information available for 3L8E)

(no "PROSITE Motif" information available for 3L8E)

(no "Exon" information available for 3L8E)

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:185
 aligned with GMHBB_ECOLI | P63228 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:185
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182     
          GMHBB_ECOLI     3 KSVPAIFLDRDGTINVDHGYVHEIDNFEFIDGVIDAMRELKKMGFALVVVTNQSGIARGKFTEAQFETLTEWMDWSLADRDVDLDGIYYCPHHPQGSVEEFRQVCDCRKPHPGMLLSARDYLHIDMAASYMVGDKLEDMQAAVAANVGTKVLVRTGKPITPEAENAADWVLNSLADLPQAIKKQQ 187
               SCOP domains d3l8ea_ A: D,D-heptose 1,7-bisphosphate phosphatase GmhB                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..............hhhhh....hhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhh.....eeeee.......hhhhh.........hhhhhhhhhhhh.hhhh.eeee.hhhhhhhhhhh...eeeee......hhhhhhh..eee.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l8e A   3 KSVPAIFLDRDGTINVDHGYVHEIDNFEFIDGVIDAMRELKKMGFALVVVTNQSGIARGKFTEAQFETLTEWMDWSLADRDVDLDGIYYCPHHPQGSVEEFRQVCDCRKPHPGMLLSARDYLHIDMAASYMVGDKLEDMQAAVAANVGTKVLVRTGKPITPEAENAADWVLNSLADLPQAIKKQQ 187
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain B from PDB  Type:PROTEIN  Length:183
 aligned with GMHBB_ECOLI | P63228 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:183
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183   
          GMHBB_ECOLI     4 SVPAIFLDRDGTINVDHGYVHEIDNFEFIDGVIDAMRELKKMGFALVVVTNQSGIARGKFTEAQFETLTEWMDWSLADRDVDLDGIYYCPHHPQGSVEEFRQVCDCRKPHPGMLLSARDYLHIDMAASYMVGDKLEDMQAAVAANVGTKVLVRTGKPITPEAENAADWVLNSLADLPQAIKKQ 186
               SCOP domains d3l8eb_ B: D,D-heptose 1,7-bisphosphate phosphatase GmhB                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..............hhhhh....hhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhh.....eeeee.......hhhhh.........hhhhhhhhhhhh.hhhh.eeee.hhhhhhhhhhh...eeeee......hhhhhhhh.eee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l8e B   4 SVPAIFLDRDGTINVDHGYVHEIDNFEFIDGVIDAMRELKKMGFALVVVTNQSGIARGKFTEAQFETLTEWMDWSLADRDVDLDGIYYCPHHPQGSVEEFRQVCDCRKPHPGMLLSARDYLHIDMAASYMVGDKLEDMQAAVAANVGTKVLVRTGKPITPEAENAADWVLNSLADLPQAIKKQ 186
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183

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: HAD-like (349)

Superfamily: HAD-like (349)

Family: Histidinol phosphatase-like (14)

Protein domain: D,D-heptose 1,7-bisphosphate phosphatase GmhB (8)

Escherichia coli [TaxId: 562] (8)

1a	d3l8ea_	A:
1b	d3l8eb_	B:

(no "CATH Domain" information available for 3L8E)

(no "Pfam Domain" information available for 3L8E)

Asymmetric Unit(hide GO term definitions)

Chain A,B (GMHBB_ECOLI | P63228)

molecular function
	GO:0034200	D,D-heptose 1,7-bisphosphate phosphatase activity	Catalysis of the reaction: D-beta-D-heptose 1,7-bisphosphate + H2O = D-beta-D-heptose 1-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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0097171	ADP-L-glycero-beta-D-manno-heptose biosynthetic process	The chemical reactions and pathways resulting in the formation of ADP-L-glycero-beta-D-manno-heptose, an ADP-L-glycero-D-manno-heptose having beta-configuration at the anomeric centre of the heptose. ADP-L-glycero-beta-D-manno-heptose (also called ADP-L-beta-D-heptose or ADP-L-glycero-D-manno-heptose) is a nucleotide-sugar precursor of the inner core lipopolysaccharide (LPS) from D-glycero-beta-D-manno-heptose 7-phosphate.
	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:0009103	lipopolysaccharide biosynthetic process	The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
	GO:0009244	lipopolysaccharide core region biosynthetic process	The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues.
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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	GMHBB_ECOLI \| P63228	:	2gmw 3esq 3esr 3l1u 3l1v 3l8f 3l8g

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SS Bonds (0, 0)

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