2GYI - JenaLib

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Title :   DESIGN, SYNTHESIS, AND CHARACTERIZATION OF A POTENT XYLOSE ISOMERASE INHIBITOR, D-THREONOHYDROXAMIC ACID, AND HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHIC STRUCTURE OF THE ENZYME-INHIBITOR COMPLEX

Authors :   K. N. Allen, A. Lavie, G. A. Petsko, D. Ringe

Date :   01 Sep 94 (Deposition) - 10 Jul 95 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Isomerase(Intramolecular Oxidoreductase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. N. Allen, A. Lavie, G. A. Petsko, D. Ringe
Design, Synthesis, And Characterization Of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, And High-Resolution X-Ray Crystallographic Structure Of The Enzyme-Inhibitor Complex
Biochemistry V. 34 3742 1995
PubMed-ID: 7893671 | Reference-DOI: 10.1021/BI00011A032
(for further references see the PDB file header)

Molecule 1 - XYLOSE ISOMERASE
	Chains	:	A, B
	EC Number	:	5.3.1.5
	Engineered	:	YES
	Organism Scientific	:	STREPTOMYCES OLIVOCHROMOGENES
	Organism Taxid	:	1963

		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	HYA	2	Ligand/Ion	2,3,4,N-TETRAHYDROXY-BUTYRIMIDIC ACID
2	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	HYA	4	Ligand/Ion	2,3,4,N-TETRAHYDROXY-BUTYRIMIDIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:180 , GLU A:216 , ASP A:244 , ASP A:286 , HYA A:960	BINDING SITE FOR RESIDUE MG A 400
02	AC2	SOFTWARE	GLU A:216 , HIS A:219 , ASP A:256 , HYA A:960 , HOH A:1700 , HOH A:1701	BINDING SITE FOR RESIDUE MG A 401
03	AC3	SOFTWARE	GLU B:180 , GLU B:216 , ASP B:244 , ASP B:286 , MG B:401 , HYA B:970	BINDING SITE FOR RESIDUE MG B 400
04	AC4	SOFTWARE	GLU B:216 , HIS B:219 , MG B:400 , HYA B:970 , HOH B:1800 , HOH B:1801	BINDING SITE FOR RESIDUE MG B 401
05	AC5	SOFTWARE	TRP A:15 , HIS A:53 , PHE A:93 , TRP A:136 , GLU A:180 , LYS A:182 , GLU A:216 , HIS A:219 , ASP A:244 , ASP A:286 , MG A:400 , MG A:401 , HOH A:1166 , HOH A:1170 , HOH A:1338 , HOH A:1700 , PHE B:25	BINDING SITE FOR RESIDUE HYA A 960
06	AC6	SOFTWARE	PHE A:25 , TRP B:15 , HIS B:53 , PHE B:93 , TRP B:136 , GLU B:180 , LYS B:182 , HIS B:219 , ASP B:244 , ASP B:286 , MG B:400 , MG B:401 , HOH B:1279 , HOH B:1281 , HOH B:1539 , HOH B:1800	BINDING SITE FOR RESIDUE HYA B 970
07	HYA	AUTHOR	HYA A:960 , LYS A:182 , HIS A:53	INHIBITOR, D-THREONOHYDROXAMIC ACID BINDING SITE IN MONOMER A
08	HYB	AUTHOR	HYA B:970 , LYS B:182 , HIS B:53	INHIBITOR, D-THREONOHYDROXAMIC ACID BINDING SITE IN MONOMER B
09	M1A	AUTHOR	MG A:400 , GLU A:180 , ASP A:244 , ASP A:286 , GLU A:216 , HYA A:960	METAL BINDING SITE 1 IN MONOMER A ACTIVE SITE
10	M1B	AUTHOR	MG B:400 , GLU B:180 , ASP B:244 , ASP B:286 , GLU B:216 , HYA B:970	METAL BINDING SITE 1 IN MONOMER B ACTIVE SITE
11	M2A	AUTHOR	MG A:401 , GLU A:216 , HIS A:219 , HYA A:960 , HOH A:1700 , HOH A:1701	METAL BINDING SITE 2 IN MONOMER A ACTIVE SITE
12	M2B	AUTHOR	MG B:401 , GLU B:216 , HIS B:219 , HYA B:970 , HOH B:1800 , HOH B:1801	METAL BINDING SITE 2 IN MONOMER B ACTIVE SITE

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

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 2GYI)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	XYLOSE_ISOMERASE	PS51415	Xylose isomerase family profile.	XYLA_STROL	4-383	2	A:3-382 B:3-382

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_STROL	4-383	4	A:3-382 B:3-382

(no "Exon" information available for 2GYI)

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
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Chain A from PDB  Type:PROTEIN  Length:385
 aligned with XYLA_STROL | P15587 from UniProtKB/Swiss-Prot  Length:387

    Alignment length:385
                                    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     
           XYLA_STROL     3 YQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAHGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAKTYVAWGGREGAESGAAKDVRVALDRMKEAFDLLGEYVTSQGYDTRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGAGDLRAAFWLVDLLESAGYEGPRHFDFKPPRTEDIDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELAQPTAADGVQELLADRTAFEDFDVDAAAARGMAFERLDQLAMDHLLGAR 387
               SCOP domains d2gyia_ A: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2gyiA00 A:2-386 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhhh...............hhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...........hhhhhhhhhh......eeeeeehhhhhhh...hhhhhhhhhhh...eeeeee..................hhhhhhhhhhhh.eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhh.......hhhhhhh........hhhhhh....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -XYLOSE_ISOMERASE  PDB: A:3-382 UniProt: 4-383                                                                                                                                                                                                                                                                                                                                               ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gyi A   2 YQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAHGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAKTYVAWGGREGAESGAAKDVRVALDRMKEAFDLLGEYVTSQGYDTRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGAGDLRAAFWLVDLLESAGYEGPRHFDFKPPRTEDIDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELAQPTAADGVQELLADRTAFEDFDVDAAAARGMAFERLDQLAMDHLLGAR 386
                                    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

Chain B from PDB  Type:PROTEIN  Length:385
 aligned with XYLA_STROL | P15587 from UniProtKB/Swiss-Prot  Length:387

    Alignment length:385
                                    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     
           XYLA_STROL     3 YQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAHGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAKTYVAWGGREGAESGAAKDVRVALDRMKEAFDLLGEYVTSQGYDTRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGAGDLRAAFWLVDLLESAGYEGPRHFDFKPPRTEDIDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELAQPTAADGVQELLADRTAFEDFDVDAAAARGMAFERLDQLAMDHLLGAR 387
               SCOP domains d2gyib_ B: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2gyiB00 B:2-386 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhhh...............hhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...........hhhhhhhhhh......eeeeeehhhhhhh...hhhhhhhhhhh...eeeeee..................hhhhhhhhhhhh.eeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhh.......hhhhhhh........hhhhhh....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -XYLOSE_ISOMERASE  PDB: B:3-382 UniProt: 4-383                                                                                                                                                                                                                                                                                                                                               ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gyi B   2 YQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAHGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAKTYVAWGGREGAESGAAKDVRVALDRMKEAFDLLGEYVTSQGYDTRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGAGDLRAAFWLVDLLESAGYEGPRHFDFKPPRTEDIDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELAQPTAADGVQELLADRTAFEDFDVDAAAARGMAFERLDQLAMDHLLGAR 386
                                    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

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

Streptomyces olivochromogenes [TaxId: 1963] (9)

1a	d2gyia_	A:
1b	d2gyib_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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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)

Streptomyces olivochromogenes. Organism_taxid: 1963 (6)

1a	2gyiA00	A:2-386
1b	2gyiB00	B:2-386

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (XYLA_STROL | P15587)

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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	2gyi
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	XYLA_STROL \| P15587
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	XYLA_STROL \| P15587	:	1muw 1s5m 1s5n 1xya 1xyb 1xyc 1xyl 1xym

(no "Related Entries Specified in the PDB File" available for 2GYI)

Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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