2I2W - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHOSPHOHEPTOSE ISOMERASE

Authors :   G. Deleon, K. Blakely, K. Zhang, G. Wright, M. Junop

Date :   17 Aug 06 (Deposition) - 21 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Lipopolysaccharide Biosynthesis, Phosphoheptose Isomerase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. L. Taylor, K. M. Blakely, G. P. De Leon, J. R. Walker, F. Mcarthur, E. Evdokimova, K. Zhang, M. A. Valvano, G. D. Wright, M. S. Junop
Structure And Function Of Sedoheptulose-7-Phosphate Isomerase, A Critical Enzyme For Lipopolysaccharide Biosynthesis And A Target For Antibiotic Adjuvants
J. Biol. Chem. V. 283 2835 2008
PubMed-ID: 18056714 | Reference-DOI: 10.1074/JBC.M706163200

Molecule 1 - PHOSPHOHEPTOSE ISOMERASE
	Chains	:	A, B, C, D
	EC Number	:	5.3.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PDEST17
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	GMHA, LPCA, TFRA, B0222
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	SEDOHEPTULOSE 7-PHOSPHATE ISOMERASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B	C
Biological Unit 3 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:89 , GLY A:92 , ASN A:93 , ASP A:94 , PHE A:97 , ASN A:98 , HOH A:193 , HOH A:237 , ARG D:135	BINDING SITE FOR RESIDUE GOL D 196

Asymmetric Unit

No.	Residues
1	A:90	-	C:90
2	B:57	-	C:57

(no "Cis Peptide Bond" information available for 2I2W)

(no "SAP(SNP)/Variant" information available for 2I2W)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIS	PS51464	SIS domain profile.	GMHA_ECOLI	37-192	4	A:37-192 B:37-192 C:37-192 D:37-192

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIS	PS51464	SIS domain profile.	GMHA_ECOLI	37-192	2	A:37-192 - - D:37-192

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIS	PS51464	SIS domain profile.	GMHA_ECOLI	37-192	2	- B:37-192 C:37-192 -

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIS	PS51464	SIS domain profile.	GMHA_ECOLI	37-192	4	A:37-192 B:37-192 C:37-192 D:37-192

(no "Exon" information available for 2I2W)

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:192
 aligned with GMHA_ECOLI | P63224 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  
           GMHA_ECOLI     1 MYQDLIRNELNEAAETLANFLKDDANIHAIQRAAVLLADSFKAGGKVLSCGNGGSHCDAMHFAEELTGRYRENRPGYPAIAISDVSHISCVGNDFGFNDIFSRYVEAVGREGDVLLGISTSGNSANVIKAIAAAREKGMKVITLTGKDGGKMAGTADIEIRVPHFGYADRIQEIHIKVIHILIQLIEKEMVK 192
               SCOP domains d2i2wa_ A: automated matches                                                                                                                                                                     SCOP domains
               CATH domains 2i2wA00 A:1-192 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhh.......eee.....hhhhhh......hhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh.eeeeeee..hhhhh....eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------SIS  PDB: A:37-192 UniProt: 37-192                                                                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2i2w A   1 MYQDLIRNELNEAAETLANFLKDDANIHAIQRAAVLLADSFKAGGKVLSCGNGGSHCDAMHFAEELTGRYRENRPGYPAIAISDVSHISCVGNDFGFNDIFSRYVEAVGREGDVLLGISTSGNSANVIKAIAAAREKGMKVITLTGKDGGKMAGTADIEIRVPHFGYADRIQEIHIKVIHILIQLIEKEMVK 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:177
 aligned with GMHA_ECOLI | P63224 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  
           GMHA_ECOLI     1 MYQDLIRNELNEAAETLANFLKDDANIHAIQRAAVLLADSFKAGGKVLSCGNGGSHCDAMHFAEELTGRYRENRPGYPAIAISDVSHISCVGNDFGFNDIFSRYVEAVGREGDVLLGISTSGNSANVIKAIAAAREKGMKVITLTGKDGGKMAGTADIEIRVPHFGYADRIQEIHIKVIHILIQLIEKEMVK 192
               SCOP domains d2i2wb_ B: automated matches                                                                                                                                                                     SCOP domains
               CATH domains 2i2wB00 B:1-192 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhh.......eee.---------------.hhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh..eeeeeee..hhhhh....eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------SIS  PDB: B:37-192 UniProt: 37-192                                                                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2i2w B   1 MYQDLIRNELNEAAETLANFLKDDANIHAIQRAAVLLADSFKAGGKVLSCGNGGSHCDAMHFAEELTGRYRENRPGYPAIAI---------------NDIFSRYVEAVGREGDVLLGISTSGNSANVIKAIAAAREKGMKVITLTGKDGGKMAGTADIEIRVPHFGYADRIQEIHIKVIHILIQLIEKEMVK 192
                                    10        20        30        40        50        60        70        80 |       -       100       110       120       130       140       150       160       170       180       190  
                                                                                                            82              98

Chain C from PDB  Type:PROTEIN  Length:192
 aligned with GMHA_ECOLI | P63224 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  
           GMHA_ECOLI     1 MYQDLIRNELNEAAETLANFLKDDANIHAIQRAAVLLADSFKAGGKVLSCGNGGSHCDAMHFAEELTGRYRENRPGYPAIAISDVSHISCVGNDFGFNDIFSRYVEAVGREGDVLLGISTSGNSANVIKAIAAAREKGMKVITLTGKDGGKMAGTADIEIRVPHFGYADRIQEIHIKVIHILIQLIEKEMVK 192
               SCOP domains d2i2wc_ C: automated matches                                                                                                                                                                     SCOP domains
               CATH domains 2i2wC00 C:1-192 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhh.......eee...................hhhhhhhhh....eeeee.....hhhhhhhhhhhhhh..eeeeeee..hhhhh....eeeee....hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------SIS  PDB: C:37-192 UniProt: 37-192                                                                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2i2w C   1 MYQDLIRNELNEAAETLANFLKDDANIHAIQRAAVLLADSFKAGGKVLSCGNGGSHCDAMHFAEELTGRYRENRPGYPAIAISDVSHISCVGNDFGFNDIFSRYVEAVGREGDVLLGISTSGNSANVIKAIAAAREKGMKVITLTGKDGGKMAGTADIEIRVPHFGYADRIQEIHIKVIHILIQLIEKEMVK 192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain D from PDB  Type:PROTEIN  Length:178
 aligned with GMHA_ECOLI | P63224 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:192
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  
           GMHA_ECOLI     1 MYQDLIRNELNEAAETLANFLKDDANIHAIQRAAVLLADSFKAGGKVLSCGNGGSHCDAMHFAEELTGRYRENRPGYPAIAISDVSHISCVGNDFGFNDIFSRYVEAVGREGDVLLGISTSGNSANVIKAIAAAREKGMKVITLTGKDGGKMAGTADIEIRVPHFGYADRIQEIHIKVIHILIQLIEKEMVK 192
               SCOP domains d2i2wd_ D: automated matches                                                                                                                                                                     SCOP domains
               CATH domains 2i2wD00 D:1-192 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhh.......eee..--------------.hhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhh..eeeeeee..hhhhh....eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------SIS  PDB: D:37-192 UniProt: 37-192                                                                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2i2w D   1 MYQDLIRNELNEAAETLANFLKDDANIHAIQRAAVLLADSFKAGGKVLSCGNGGSHCDAMHFAEELTGRYRENRPGYPAIAIS--------------NDIFSRYVEAVGREGDVLLGISTSGNSANVIKAIAAAREKGMKVITLTGKDGGKMAGTADIEIRVPHFGYADRIQEIHIKVIHILIQLIEKEMVK 192
                                    10        20        30        40        50        60        70        80  |      -       100       110       120       130       140       150       160       170       180       190  
                                                                                                             83             98

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: SIS domain (85)

Superfamily: SIS domain (85)

Family: automated matches (22)

Protein domain: automated matches (22)

Escherichia coli [TaxId: 562] (2)

1a	d2i2wa_	A:
1b	d2i2wb_	B:
1c	d2i2wc_	C:
1d	d2i2wd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Glucose-6-phosphate isomerase like protein; domain 1 (105)

Escherichia coli. Organism_taxid: 562. (3)

1a	2i2wA00	A:1-192
1b	2i2wC00	C:1-192
1c	2i2wD00	D:1-192
1d	2i2wB00	B:1-192

(no "Pfam Domain" information available for 2I2W)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (GMHA_ECOLI | P63224)

molecular function
	GO:0008968	D-sedoheptulose 7-phosphate isomerase activity	Catalysis of the reaction: D-sedoheptulose-7-phosphate = D-alpha,beta-D-heptose 7-phosphate.
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:2001061	D-glycero-D-manno-heptose 7-phosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of a D-glycero-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: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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	GMHA_ECOLI \| P63224	:	2i22

2i22	CRYSTAL STRUCTURE OF ESCHERICHIA COLI PHOSPHOHEPTOSE ISOMERASE IN COMPLEX WITH REACTION SUBSTRATE SEDOHEPTULOSE 7-PHOSPHATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

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