1XLM - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   D254E, D256E MUTANT OF D-XYLOSE ISOMERASE COMPLEXED WITH AL3 AND XYLITOL

Authors :   T. Gerczei, Z. S. Bocskei, E. Szabo, G. Naray-Szabo, B. Asboth

Date :   22 Jul 97 (Deposition) - 28 Jan 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Isomerase, Al, Substrate Induced Metal Ion Movement, Xylose Metabolism, Pentose Shunt (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Gerczei, Z. Bocskei, E. Szabo, B. Asboth, G. Naray-Szabo
Structure Determination And Refinement Of The Al3+ Complex Of The D254, 256E Mutant Of Arthrobacter D-Xylose Isomerase At 2. 40 A Resolution. Further Evidence For Inhibitor-Induce Metal Ion Movement.
Int. J. Biol. Macromol. V. 25 329 1999
PubMed-ID: 10456773 | Reference-DOI: 10.1016/S0141-8130(99)00051-3
(for further references see the PDB file header)

Molecule 1 - D-XYLOSE ISOMERASE
	Chains	:	A, B
	EC Number	:	5.3.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	SECRETION
	Expression System Plasmid	:	PAXI3
	Expression System Strain	:	JM101
	Expression System Taxid	:	562
	Expression System Vector	:	PTZ19U
	Mutation	:	YES
	Organism Scientific	:	ARTHROBACTER SP. NRRL
	Organism Taxid	:	1669
	Strain	:	B3728

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	AL	4	Ligand/Ion	ALUMINUM ION
2	XYL	2	Ligand/Ion	D-XYLITOL

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	AL	-1	Ligand/Ion	ALUMINUM ION
2	XYL	4	Ligand/Ion	D-XYLITOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:15 , PHE A:25 , HIS A:53 , TRP A:136 , GLU A:180 , LYS A:182 , GLU A:216 , HIS A:219 , ASP A:244 , GLU A:254 , GLU A:256 , ASP A:292 , AL A:398 , AL A:399	BINDING SITE FOR RESIDUE XYL A 400
2	AC2	SOFTWARE	TRP B:15 , PHE B:25 , HIS B:53 , TRP B:136 , GLU B:180 , GLU B:216 , HIS B:219 , ASP B:244 , GLU B:254 , GLU B:256 , ASP B:292 , AL B:398 , AL B:399	BINDING SITE FOR RESIDUE XYL B 400
3	AC3	SOFTWARE	GLU A:180 , GLU A:216 , ASP A:244 , ASP A:292 , AL A:399 , XYL A:400	BINDING SITE FOR RESIDUE AL A 398
4	AC4	SOFTWARE	GLU A:216 , HIS A:219 , GLU A:254 , GLU A:256 , ASP A:292 , AL A:398 , XYL A:400	BINDING SITE FOR RESIDUE AL A 399
5	AC5	SOFTWARE	GLU B:180 , GLU B:216 , ASP B:244 , ASP B:292 , AL B:399 , XYL B:400	BINDING SITE FOR RESIDUE AL B 398
6	AC6	SOFTWARE	GLU B:216 , HIS B:219 , GLU B:254 , GLU B:256 , ASP B:292 , AL B:398 , XYL B:400	BINDING SITE FOR RESIDUE AL B 399
7	CTA	UNKNOWN	THR B:16 , ASP B:54 , LEU B:57 , SER B:94 , GLY B:137 , PRO B:181 , PRO B:183 , PRO B:186 , GLU A:220 , LEU A:245 , GLN A:255 , LEU A:257 , GLY A:287	CATALYTIC SITE.
8	CTB	UNKNOWN	THR B:16 , ASP B:54 , LEU B:57 , SER B:94 , GLY B:137 , PRO B:181 , PRO B:183 , PRO B:186 , GLU B:220 , LEU B:245 , GLN B:255 , LEU B:257 , GLY B:287	CATALYTIC SITE.

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

Asymmetric Unit

No.	Residues
1	Glu A:185	-	Pro A:186
2	Glu B:185	-	Pro B:186

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	XYLOSE_ISOMERASE	PS51415	Xylose isomerase family profile.	XYLA_ARTS7	4-391	2	A:3-390 B:3-390

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_ARTS7	4-391	4	A:3-390 B:3-390

(no "Exon" information available for 1XLM)

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:393
 aligned with XYLA_ARTS7 | P12070 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:393
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392   
           XYLA_ARTS7     3 VQPTPADHFTFGLWTVGWTGADPFGVATRKNLDPVEAVHKLAELGAYGITFHDNDLIPFDATEAEREKILGDFNQALKDTGLKVPMVTTNLFSHPVFKDGGFTSNDRSIRRFALAKVLHNIDLAAEMGAETFVMWGGREGSEYDGSKDLAAALDRMREGVDTAAGYIKDKGYNLRIALEPKPNEPRGDIFLPTVGHGLAFIEQLEHGDIVGLNPETGHEQMAGLNFTHGIAQALWAEKLFHIDLNGQRGIKYDQDLVFGHGDLTSAFFTVDLLENGFPNGGPKYTGPRHFDYKPSRTDGYDGVWDSAKANMSMYLLLKERALAFRADPEVQEAMKTSGVFELGETTLNAGESAADLMNDSASFAGFDAEAAAERNFAFIRLNQLAIEHLLGSR 395
               SCOP domains d1xlma_ A: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1xlmA00 A:2-394 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeehhhh.................hhhhhhhhhhh...eeeeehhhh......hhhhhhhhhhhhhhhhhh.....eee......hhh.........hhhhhhhhhhhhhhhhhhhhh...eeee.........hhh..hhhhhhhhhhhhhhhhhhhhhh....eeee...............hhhhhhhhhh...hhheeeeeehhhhhhh...hhhhhhhhhh...eeeee...................hhhhhhhhhhhhh............eee.........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh...hhh.........hhhhh..hhh.....hhhhhh....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -XYLOSE_ISOMERASE  PDB: A:3-390 UniProt: 4-391                                                                                                                                                                                                                                                                                                                                                       ---- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xlm A   2 VQPTPADHFTFGLWTVGWTGADPFGVATRKNLDPVEAVHKLAELGAYGITFHDNDLIPFDATEAEREKILGDFNQALKDTGLKVPMVTTNLFSHPVFKDGGFTSNDRSIRRFALAKVLHNIDLAAEMGAETFVMWGGREGSEYDGSKDLAAALDRMREGVDTAAGYIKDKGYNLRIALEPKPNEPRGDIFLPTVGHGLAFIEQLEHGDIVGLNPETGHEQMAGLNFTHGIAQALWAEKLFHIDLNGQRGIKYEQELVFGHGDLTSAFFTVDLLENGFPNGGPKYTGPRHFDYKPSRTDGYDGVWDSAKANMSMYLLLKERALAFRADPEVQEAMKTSGVFELGETTLNAGESAADLMNDSASFAGFDAEAAAERNFAFIRLNQLAIEHLLGSR 394
                                    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

Chain B from PDB  Type:PROTEIN  Length:393
 aligned with XYLA_ARTS7 | P12070 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:393
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392   
           XYLA_ARTS7     3 VQPTPADHFTFGLWTVGWTGADPFGVATRKNLDPVEAVHKLAELGAYGITFHDNDLIPFDATEAEREKILGDFNQALKDTGLKVPMVTTNLFSHPVFKDGGFTSNDRSIRRFALAKVLHNIDLAAEMGAETFVMWGGREGSEYDGSKDLAAALDRMREGVDTAAGYIKDKGYNLRIALEPKPNEPRGDIFLPTVGHGLAFIEQLEHGDIVGLNPETGHEQMAGLNFTHGIAQALWAEKLFHIDLNGQRGIKYDQDLVFGHGDLTSAFFTVDLLENGFPNGGPKYTGPRHFDYKPSRTDGYDGVWDSAKANMSMYLLLKERALAFRADPEVQEAMKTSGVFELGETTLNAGESAADLMNDSASFAGFDAEAAAERNFAFIRLNQLAIEHLLGSR 395
               SCOP domains d1xlmb_ B: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1xlmB00 B:2-394 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) -------------------------------------AP_endonuc_2-1xlmB01 B:39-264                                                                                                                                                                                                     ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------AP_endonuc_2-1xlmB02 B:39-264                                                                                                                                                                                                     ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhh.eeeehhhh.................hhhhhhhhhhh...eeeeehhhh......hhhhhhhhhhhhhhhhhh.....eee......hhh.........hhhhhhhhhhhhhhhhhhhhh...eeee.........hhh..hhhhhhhhhhhhhhhhhhhhhh....eeee...............hhhhhhhhhh...hhheeeeeehhhhhhh...hhhhhhhhhh...eeeee...................hhhhhhhhhhhhh............eee.........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh...hhh.........hhhhh..hhh.....hhhhhh....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -XYLOSE_ISOMERASE  PDB: B:3-390 UniProt: 4-391                                                                                                                                                                                                                                                                                                                                                       ---- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xlm B   2 VQPTPADHFTFGLWTVGWTGADPFGVATRKNLDPVEAVHKLAELGAYGITFHDNDLIPFDATEAEREKILGDFNQALKDTGLKVPMVTTNLFSHPVFKDGGFTSNDRSIRRFALAKVLHNIDLAAEMGAETFVMWGGREGSEYDGSKDLAAALDRMREGVDTAAGYIKDKGYNLRIALEPKPNEPRGDIFLPTVGHGLAFIEQLEHGDIVGLNPETGHEQMAGLNFTHGIAQALWAEKLFHIDLNGQRGIKYEQELVFGHGDLTSAFFTVDLLENGFPNGGPKYTGPRHFDYKPSRTDGYDGVWDSAKANMSMYLLLKERALAFRADPEVQEAMKTSGVFELGETTLNAGESAADLMNDSASFAGFDAEAAAERNFAFIRLNQLAIEHLLGSR 394
                                    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

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)

Arthrobacter, strain b3728 [TaxId: 1663] (17)

1a	d1xlma_	A:
1b	d1xlmb_	B:

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)

Nrrl b3728 (Arthrobacter sp) (17)

1a	1xlmA00	A:2-394
1b	1xlmB00	B:2-394

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: AP_endonuc_2 (72)

Arthrobacter sp. (strain NRRL B3728) (11)

1a	AP_endonuc_2-1xlmB01	B:39-264
1b	AP_endonuc_2-1xlmB02	B:39-264

Asymmetric Unit(hide GO term definitions)

Chain A,B (XYLA_ARTS7 | P12070)

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:185 - Pro A:186	[ RasMol ]
		Glu B:185 - Pro B:186	[ RasMol ]

Biological Unit
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	1xlm
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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