1A0E - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   XYLOSE ISOMERASE FROM THERMOTOGA NEAPOLITANA

Authors :   O. Gallay, R. Chopra, E. Conti, P. Brick, D. Blow

Date :   28 Nov 97 (Deposition) - 03 Jun 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Ketolisomerase, Xylose Metabolism, Glucose-Fructose Interconversion, Hydride Transfer, Alpha-Beta Barrel, Metalloenzyme, Thermophile (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Gallay, R. Chopra, E. Conti, P. Brick, R. Jackson, B. Hartley, C. Vieille, J. G. Zeikus, D. Blow
Crystal Structures Of Class Ii Xylose Isomerases From Two Thermophiles And A Hyperthermophile
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - XYLOSE ISOMERASE
	Cellular Location	:	CYTOPLASM
	Chains	:	A, D
	EC Number	:	5.3.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Gene	:	XYLA
	Expression System Plasmid	:	PTNE2
	Expression System Strain	:	HB101
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	XYLA
	Organism Scientific	:	THERMOTOGA NEAPOLITANA
	Organism Taxid	:	2337
	Strain	:	5068
	Synonym	:	GLUCOSE ISOMERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	CO	6	Ligand/Ion	COBALT (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:231 , GLU A:267 , ASP A:295 , ASP A:338 , HOH A:613	BINDING SITE FOR RESIDUE CO A 491
02	AC2	SOFTWARE	GLU A:267 , HIS A:270 , ASP A:306 , ASP A:308 , HOH A:613 , HOH A:614 , HOH A:615 , HOH A:616	BINDING SITE FOR RESIDUE CO A 492
03	AC3	SOFTWARE	GLU A:2	BINDING SITE FOR RESIDUE CO A 493
04	AC4	SOFTWARE	GLU D:231 , GLU D:267 , ASP D:295 , ASP D:338 , HOH D:618	BINDING SITE FOR RESIDUE CO D 491
05	AC5	SOFTWARE	GLU D:267 , HIS D:270 , ASP D:306 , ASP D:308 , HOH D:618 , HOH D:619 , HOH D:620 , HOH D:621	BINDING SITE FOR RESIDUE CO D 492
06	AC6	SOFTWARE	GLU D:2	BINDING SITE FOR RESIDUE CO D 493
07	CO1	UNKNOWN	GLU A:231 , GLU A:267 , ASP A:295 , ASP A:338 , HOH A:614	CO BINDING SITE 1 OF MOLECULE A
08	CO2	UNKNOWN	GLU A:267 , HIS A:270 , HOH A:614 , HOH A:615 , HOH A:616	CO BINDING SITE 2 OF MOLECULE A (HOH629 WAS ADDED AFTER LAST REFINEMENT RESULTED IN A NEW FO-FC PEAK AT THIS SITE).
09	CO3	UNKNOWN	GLU A:2	CO BINDING SITE 3 OF MOLECULE A (SITE CO3 IS ON A CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY AXIS: INTERPRETATION OF THE OBSERVED DENSITY PEAK AS A CO CATION WAS PRAGMATIC RATHER THAN RIGOROUS, AS THIS SITE IS CLEARLY NOT A FEATURE OF THE PROTEIN IN SOLUTION).
10	CO4	UNKNOWN	GLU D:231 , GLU D:267 , ASP D:295 , ASP D:338 , HOH D:619	CO BINDING SITE 1 OF MOLECULE D
11	CO5	UNKNOWN	GLU D:267 , HIS D:270 , HOH D:619 , HOH D:620 , HOH D:621	CO BINDING SITE 2 OF MOLECULE D (HOH629 WAS ADDED AFTER LAST REFINEMENT RESULTED IN A NEW FO-FC PEAK AT THIS SITE).
12	CO6	UNKNOWN	GLU D:2	CO BINDING SITE 3 OF MOLECULE D (SITE CO3 IS ON A CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY AXIS: INTERPRETATION OF THE OBSERVED DENSITY PEAK AS A CO CATION WAS PRAGMATIC RATHER THAN RIGOROUS, AS THIS SITE IS CLEARLY NOT A FEATURE OF THE PROTEIN IN SOLUTION).

(no "SS Bond" information available for 1A0E)

Asymmetric Unit

No.	Residues
1	Glu A:236	-	Pro A:237
2	Glu D:236	-	Pro D:237

(no "SAP(SNP)/Variant" information available for 1A0E)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	XYLOSE_ISOMERASE	PS51415	Xylose isomerase family profile.	XYLA_THENE	35-436	2	A:34-435 D:34-435

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	XYLOSE_ISOMERASE	PS51415	Xylose isomerase family profile.	XYLA_THENE	35-436	4	A:34-435 D:34-435

(no "Exon" information available for 1A0E)

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:443
 aligned with XYLA_THENE | P45687 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:443
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441   
           XYLA_THENE     2 AEFFPEIPKVQFEGKESTNPLAFKFYDPEEIIDGKPLKDHLKFSVAFWHTFVNEGRDPFGDPTADRPWNRYTDPMDKAFARVDALFEFCEKLNIEYFCFHDRDIAPEGKTLRETNKILDKVVERIKERMKDSNVKLLWGTANLFSHPRYMHGAATTCSADVFAYAAAQVKKALEITKELGGEGYVFWGGREGYETLLNTDLGFELENLARFLRMAVDYAKRIGFTGQFLIEPKPKEPTKHQYDFDVATAYAFLKSHGLDEYFKFNIEANHATLAGHTFQHELRMARILGKLGSIDANQGDLLLGWDTDQFPTNVYDTTLAMYEVIKAGGFTKGGLNFDAKVRRASYKVEDLFIGHIAGMDTFALGFKVAYKLVKDGVLDKFIEEKYRSFREGIGRDIVEGKVDFEKLEEYIIDKETIELPSGKQEYLESLINSYIVKTILELR 444
               SCOP domains d1a0ea_ A: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1a0eA00 A:1-443 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................................hhhhh.....hhhh................hhh....hhhhhhhhhhhhhhhhhhh........hhhh......hhhhhhhhhhhhhhhhhhhhh......eee......hhh.........hhhhhhhhhhhhhhhhhhhh....eeee..............hhhhhhhhhhhhhhhhhhhhhh....eeee...............hhhhhhhhhhh..hhheeeeeehhhhhh....hhhhhhhhhh...eeeee..................hhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhh..hhhhhhhh....hhhhhhhh............hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------XYLOSE_ISOMERASE  PDB: A:34-435 UniProt: 35-436                                                                                                                                                                                                                                                                                                                                                                   -------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a0e A   1 AEFFPEIPKVQFEGKESTNPLAFKFYDPEEIIDGKPLKDHLKFSVAFWHTFVNEGRDPFGDPTADRPWNRYTDPMDKAFARVDALFEFCEKLNIEYFCFHDRDIAPEGKTLRETNKILDKVVERIKERMKDSNVKLLWGTANLFSHPRYMHGAATTCSADVFAYAAAQVKKALEITKELGGEGYVFWGGREGYETLLNTDLGFELENLARFLRMAVDYAKRIGFTGQFLIEPKPKEPTKHQYDFDVATAYAFLKSHGLDEYFKFNIEANHATLAGHTFQHELRMARILGKLGSIDANQGDLLLGWDTDQFPTNVYDTTLAMYEVIKAGGFTKGGLNFDAKVRRASYKVEDLFIGHIAGMDTFALGFKVAYKLVKDGVLDKFIEEKYRSFREGIGRDIVEGKVDFEKLEEYIIDKETIELPSGKQEYLESLINSYIVKTILELR 443
                                    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       330       340       350       360       370       380       390       400       410       420       430       440

Chain D from PDB  Type:PROTEIN  Length:443
 aligned with XYLA_THENE | P45687 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:443
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441   
           XYLA_THENE     2 AEFFPEIPKVQFEGKESTNPLAFKFYDPEEIIDGKPLKDHLKFSVAFWHTFVNEGRDPFGDPTADRPWNRYTDPMDKAFARVDALFEFCEKLNIEYFCFHDRDIAPEGKTLRETNKILDKVVERIKERMKDSNVKLLWGTANLFSHPRYMHGAATTCSADVFAYAAAQVKKALEITKELGGEGYVFWGGREGYETLLNTDLGFELENLARFLRMAVDYAKRIGFTGQFLIEPKPKEPTKHQYDFDVATAYAFLKSHGLDEYFKFNIEANHATLAGHTFQHELRMARILGKLGSIDANQGDLLLGWDTDQFPTNVYDTTLAMYEVIKAGGFTKGGLNFDAKVRRASYKVEDLFIGHIAGMDTFALGFKVAYKLVKDGVLDKFIEEKYRSFREGIGRDIVEGKVDFEKLEEYIIDKETIELPSGKQEYLESLINSYIVKTILELR 444
               SCOP domains d1a0ed_ D: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1a0eD00 D:1-443 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................................hhhhh.....hhhh................hhh....hhhhhhhhhhhhhhhhhhh........hhhh......hhhhhhhhhhhhhhhhhhhhh......eee......hhh.........hhhhhhhhhhhhhhhhhhhh....eeee..............hhhhhhhhhhhhhhhhhhhhhh....eeee...............hhhhhhhhhhh..hhheeeeeehhhhhh....hhhhhhhhhh...eeeee..................hhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhh..hhhhhhhh....hhhhhhhh............hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------XYLOSE_ISOMERASE  PDB: D:34-435 UniProt: 35-436                                                                                                                                                                                                                                                                                                                                                                   -------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a0e D   1 AEFFPEIPKVQFEGKESTNPLAFKFYDPEEIIDGKPLKDHLKFSVAFWHTFVNEGRDPFGDPTADRPWNRYTDPMDKAFARVDALFEFCEKLNIEYFCFHDRDIAPEGKTLRETNKILDKVVERIKERMKDSNVKLLWGTANLFSHPRYMHGAATTCSADVFAYAAAQVKKALEITKELGGEGYVFWGGREGYETLLNTDLGFELENLARFLRMAVDYAKRIGFTGQFLIEPKPKEPTKHQYDFDVATAYAFLKSHGLDEYFKFNIEANHATLAGHTFQHELRMARILGKLGSIDANQGDLLLGWDTDQFPTNVYDTTLAMYEVIKAGGFTKGGLNFDAKVRRASYKVEDLFIGHIAGMDTFALGFKVAYKLVKDGVLDKFIEEKYRSFREGIGRDIVEGKVDFEKLEEYIIDKETIELPSGKQEYLESLINSYIVKTILELR 443
                                    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       330       340       350       360       370       380       390       400       410       420       430       440

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: TIM beta/alpha-barrel (3956)

Superfamily: Xylose isomerase-like (125)

Family: Xylose isomerase (97)

Protein domain: D-xylose isomerase (82)

Thermotoga neapolitana [TaxId: 2337] (1)

1a	d1a0ea_	A:
1b	d1a0ed_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Divalent-metal-dependent TIM barrel enzymes (98)

Thermotoga neapolitana. Organism_taxid: 2337. Strain: 5068. (1)

1a	1a0eA00	A:1-443
1b	1a0eD00	D:1-443

(no "Pfam Domain" information available for 1A0E)

Asymmetric Unit(hide GO term definitions)

Chain A,D (XYLA_THENE | P45687)

molecular function
	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: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:0009045	xylose isomerase activity	Catalysis of the reaction: D-xylose = D-xylulose.
biological process
	GO:0042732	D-xylose metabolic process	The chemical reactions and pathways involving D-xylose, a naturally occurring plant polysaccharide.
	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:0006098	pentose-phosphate shunt	The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:236 - Pro A:237	[ RasMol ]
		Glu D:236 - Pro D:237	[ RasMol ]

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	1a0e
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Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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