2XHZ - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   PROBING THE ACTIVE SITE OF THE SUGAR ISOMERASE DOMAIN FROM E. COLI ARABINOSE-5-PHOSPHATE ISOMERASE VIA X-RAY CRYSTALLOGRAPHY

Authors :   L. J. Gourlay, S. Sommaruga, M. Nardini, P. Sperandeo, G. Deho, A. Polis M. Bolognesi

Date :   24 Jun 10 (Deposition) - 26 Jan 11 (Release) - 13 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

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

Reference :   L. J. Gourlay, S. Sommaruga, M. Nardini, P. Sperandeo, G. Deho, A. Polissi, M. Bolognesi
Probing The Active Site Of The Sugar Isomerase Domain From E. Coli Arabinose-5-Phosphate Isomerase Via X-Ray Crystallography.
Protein Sci. V. 19 2430 2010
PubMed-ID: 20954237 | Reference-DOI: 10.1002/PRO.525

Molecule 1 - ARABINOSE 5-PHOSPHATE ISOMERASE
	Chains	:	A, B, C, D
	EC Number	:	5.3.1.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	SUGAR ISOMERASE DOMAIN, RESIDUES 1-183
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	KDSD, YRBH

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2XHZ)

(no "Site" information available for 2XHZ)

(no "SS Bond" information available for 2XHZ)

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIS	PS51464	SIS domain profile.	KDSD_ECOLI	42-184	4	A:42-183 B:42-183 C:42-183 D:42-182

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIS	PS51464	SIS domain profile.	KDSD_ECOLI	42-184	4	A:42-183 B:42-183 C:42-183 D:42-182

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIS	PS51464	SIS domain profile.	KDSD_ECOLI	42-184	2	A:42-183 B:42-183 - -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SIS	PS51464	SIS domain profile.	KDSD_ECOLI	42-184	2	- - C:42-183 D:42-182

(no "Exon" information available for 2XHZ)

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:173
 aligned with KDSD_ECOLI | P45395 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:173
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   
           KDSD_ECOLI    11 DFQQAGKEVLAIERECLAELDQYINQNFTLACEKMFWCKGKVVVMGMGKSGHIGRKMAATFASTGTPSFFVHPGEAAHGDLGMVTPQDVVIAISNSGESSEITALIPVLKRLHVPLICITGRPESSMARAADVHLCVKVAKEACPLGLAPTSSTTATLVMGDALAVALLKARG 183
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhh....eee...hhhhhhh........eeeee.....hhhhhhhhhhhhh....eeeee....hhhhhhh.eeee..............hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------SIS  PDB: A:42-183 UniProt: 42-184                                                                                                             PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xhz A  11 DFQQAGKEVLAIERECLAELDQYINQNFTLACEKMFWCKGKVVVMGMGASGHIGRKMAATFASTGTPSFFVHPGEAAHGDLGMVTPQDVVIAISNSGESSEITALIPVLKRLHVPLICITGRPESSMARAADVHLCVKVAKEACPLGLAPTSSTTATLVMGDALAVALLKARG 183
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:174
 aligned with KDSD_ECOLI | P45395 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:174
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179    
           KDSD_ECOLI    10 FDFQQAGKEVLAIERECLAELDQYINQNFTLACEKMFWCKGKVVVMGMGKSGHIGRKMAATFASTGTPSFFVHPGEAAHGDLGMVTPQDVVIAISNSGESSEITALIPVLKRLHVPLICITGRPESSMARAADVHLCVKVAKEACPLGLAPTSSTTATLVMGDALAVALLKARG 183
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhh....eee.hhhhhhhh.........eeeee.....hhhhhhhhhhhhh....eeeee....hhhhhhh.eeee..............hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------SIS  PDB: B:42-183 UniProt: 42-184                                                                                                             PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xhz B  10 FDFQQAGKEVLAIERECLAELDQYINQNFTLACEKMFWCKGKVVVMGMGASGHIGRKMAATFASTGTPSFFVHPGEAAHGDLGMVTPQDVVIAISNSGESSEITALIPVLKRLHVPLICITGRPESSMARAADVHLCVKVAKEACPLGLAPTSSTTATLVMGDALAVALLKARG 183
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179

Chain C from PDB  Type:PROTEIN  Length:173
 aligned with KDSD_ECOLI | P45395 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:173
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   
           KDSD_ECOLI    11 DFQQAGKEVLAIERECLAELDQYINQNFTLACEKMFWCKGKVVVMGMGKSGHIGRKMAATFASTGTPSFFVHPGEAAHGDLGMVTPQDVVIAISNSGESSEITALIPVLKRLHVPLICITGRPESSMARAADVHLCVKVAKEACPLGLAPTSSTTATLVMGDALAVALLKARG 183
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhh..eee.hhhhhhhh.........eeeee.....hhhhhhhhhhhhh....eeeee....hhhhhh..eeee..............hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------SIS  PDB: C:42-183 UniProt: 42-184                                                                                                             PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xhz C  11 DFQQAGKEVLAIERECLAELDQYINQNFTLACEKMFWCKGKVVVMGMGASGHIGRKMAATFASTGTPSFFVHPGEAAHGDLGMVTPQDVVIAISNSGESSEITALIPVLKRLHVPLICITGRPESSMARAADVHLCVKVAKEACPLGLAPTSSTTATLVMGDALAVALLKARG 183
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain D from PDB  Type:PROTEIN  Length:173
 aligned with KDSD_ECOLI | P45395 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:173
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179   
           KDSD_ECOLI    10 FDFQQAGKEVLAIERECLAELDQYINQNFTLACEKMFWCKGKVVVMGMGKSGHIGRKMAATFASTGTPSFFVHPGEAAHGDLGMVTPQDVVIAISNSGESSEITALIPVLKRLHVPLICITGRPESSMARAADVHLCVKVAKEACPLGLAPTSSTTATLVMGDALAVALLKAR 182
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------SIS-2xhzD01 D:45-177                                                                                                                 ----- Pfam domains (1)
           Pfam domains (2) -----------------------------------SIS-2xhzD02 D:45-177                                                                                                                 ----- Pfam domains (2)
           Pfam domains (3) -----------------------------------SIS-2xhzD03 D:45-177                                                                                                                 ----- Pfam domains (3)
           Pfam domains (4) -----------------------------------SIS-2xhzD04 D:45-177                                                                                                                 ----- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhh...eee.hhhhhhhhh........eeeee.....hhhhhhhhhhhhh....eeeee....hhhhhhh.eeee..............hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------SIS  PDB: D:42-182 UniProt: 42-184                                                                                                            PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xhz D  10 FDFQQAGKEVLAIERECLAELDQYINQNFTLACEKMFWCKGKVVVMGMGASGHIGRKMAATFASTGTPSFFVHPGEAAHGDLGMVTPQDVVIAISNSGESSEITALIPVLKRLHVPLICITGRPESSMARAADVHLCVKVAKEACPLGLAPTSSTTATLVMGDALAVALLKAR 182
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179

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 '\|'

(no "SCOP Domain" information available for 2XHZ)

(no "CATH Domain" information available for 2XHZ)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: SIS (53)

Family: SIS (23)

Escherichia coli (strain K12) (7)

1a	SIS-2xhzD01	D:45-177
1b	SIS-2xhzD02	D:45-177
1c	SIS-2xhzD03	D:45-177
1d	SIS-2xhzD04	D:45-177

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (KDSD_ECOLI | P45395)

molecular function
	GO:0019146	arabinose-5-phosphate isomerase activity	Catalysis of the reaction: D-arabinose 5-phosphate = D-ribulose 5-phosphate + 2 H(+).
	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.
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:0019294	keto-3-deoxy-D-manno-octulosonic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of keto-3-deoxy-D-manno-octulosonic acid, an acidic sugar present in lipopolysaccharides of the outer membranes of some Gram-negative bacteria.
	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.

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Biological Units
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	2xhz
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