1OAD - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   GLUCOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS IN P21212 CRYSTAL FORM

Authors :   U. A. Ramagopal, M. Dauter, Z. Dauter

Date :   08 Jan 03 (Deposition) - 30 Jan 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Isomerase, Glucose Isomerase, Xylose Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. A. Ramagopal, M. Dauter, Z. Dauter
Sad Manganese In Two Crystal Forms Of Glucose Isomerase
Acta Crystallogr. , Sect. D V. 59 868 2003
PubMed-ID: 12777803 | Reference-DOI: 10.1107/S0907444903005663

Molecule 1 - XYLOSE ISOMERASE
	Chains	:	A, B
	EC Number	:	5.3.1.5
	Organism Scientific	:	STREPTOMYCES RUBIGINOSUS
	Organism Taxid	:	1929
	Synonym	:	GLUCOSE ISOMERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 10)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	MN	2	Ligand/Ion	MANGANESE (II) ION
3	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
4	MQD	2	Ligand/Ion	2-METHYLPENTANE-1,2,4-TRIOL
5	MRD	2	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
6	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (4, 12)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
4	MQD	4	Ligand/Ion	2-METHYLPENTANE-1,2,4-TRIOL
5	MRD	4	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
6	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:217 , HIS A:220 , ASP A:255 , ASP A:257 , HOH A:2464	BINDING SITE FOR RESIDUE MN A 390
02	AC2	SOFTWARE	GLU A:181 , GLU A:217 , ASP A:245 , ASP A:287 , MQD A:395 , HOH A:2321	BINDING SITE FOR RESIDUE MG A 392
03	AC3	SOFTWARE	GLU B:217 , HIS B:220 , ASP B:255 , ASP B:257 , HOH B:2432	BINDING SITE FOR RESIDUE MN B 390
04	AC4	SOFTWARE	GLU B:181 , GLU B:217 , ASP B:245 , ASP B:287 , MQD B:395 , HOH B:2293	BINDING SITE FOR RESIDUE MG B 392
05	AC5	SOFTWARE	HOH A:2465 , HOH A:2467 , HIS B:54 , THR B:95	BINDING SITE FOR RESIDUE MRD A 394
06	AC6	SOFTWARE	TRP A:16 , HIS A:54 , PHE A:94 , TRP A:137 , GLU A:181 , GLU A:217 , HIS A:220 , ASP A:287 , MG A:392 , HOH A:2464 , HOH A:2468 , HOH A:2469	BINDING SITE FOR RESIDUE MQD A 395
07	AC7	SOFTWARE	TYR A:3 , GLU A:70 , LYS A:73 , GLU A:315 , HOH A:2116 , HOH A:2130 , HOH A:2470 , HOH A:2471 , HOH A:2472 , HOH A:2473 , HOH A:2474 , GLY B:385 , HOH B:2429	BINDING SITE FOR RESIDUE TRS A 396
08	AC8	SOFTWARE	HIS A:54 , THR A:95 , PRO B:25 , PHE B:26 , HOH B:2433 , HOH B:2435	BINDING SITE FOR RESIDUE MRD B 394
09	AC9	SOFTWARE	TRP B:16 , HIS B:54 , PHE B:94 , TRP B:137 , GLU B:181 , GLU B:217 , HIS B:220 , ASP B:287 , MG B:392 , HOH B:2432 , HOH B:2436 , HOH B:2437	BINDING SITE FOR RESIDUE MQD B 395
10	BC1	SOFTWARE	ARG A:331 , ASP A:336 , GLU A:337 , HOH A:2063 , HOH A:2189	BINDING SITE FOR RESIDUE MPD B 396

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

Asymmetric Unit

No.	Residues
1	Glu A:186	-	Pro A:187
2	Glu B:186	-	Pro B:187

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

Asymmetric Unit (1, 2)

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

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_STRRU	4-383	4	A:4-383 B:4-383

(no "Exon" information available for 1OAD)

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:387
 aligned with XYLA_STRRU | P24300 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:387
                                    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       
           XYLA_STRRU     2 NYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG 388
               SCOP domains d1oada_ A: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1oadA00 A:2-388 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.eeeehhhhh...............hhhhhhhhhhhh...eeeeehhhhh....hhhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhh...eeee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.........ee...hhhhhhhhhh...hhh.eee..hhhhhhh...hhhhhhhhhhhh......ee.................hhhhhhhhhhhhhhh.....eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --XYLOSE_ISOMERASE  PDB: A:4-383 UniProt: 4-383                                                                                                                                                                                                                                                                                                                                               ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oad A   2 NYQPTPEDRFTFGLWTVGWEGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG 388
                                    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:386
 aligned with XYLA_STRRU | P24300 from UniProtKB/Swiss-Prot  Length:388

    Alignment length: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      
           XYLA_STRRU     2 NYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGAR 387
               SCOP domains d1oadb_ B: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1oadB00 B:2-387 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                        CATH domains
           Pfam domains (1) --------------------------------------AP_endonuc_2-1oadB01 B:40-265                                                                                                                                                                                                     -------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------AP_endonuc_2-1oadB02 B:40-265                                                                                                                                                                                                     -------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhh.eeeehhhhh...............hhhhhhhhhhhh...eeeeehhhhh....hhhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhh...eeee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.........ee...hhhhhhhhhh...hhh.eee..hhhhhhh...hhhhhhhhhhhh......ee.................hhhhhhhhhhhhhhh.....eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --XYLOSE_ISOMERASE  PDB: B:4-383 UniProt: 4-383                                                                                                                                                                                                                                                                                                                                               ---- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oad B   2 NYQPTPEDRFTFGLWTVGWEGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGAR 387
                                    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(

)

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)

Streptomyces rubiginosus [TaxId: 1929] (31)

1a	d1oada_	A:
1b	d1oadb_	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)

Streptomyces rubiginosus. Organism_taxid: 1929 (21)

1a	1oadB00	B:2-387
1b	1oadA00	A:2-388

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: AP_endonuc_2 (72)

Streptomyces rubiginosus (22)

1a	AP_endonuc_2-1oadB01	B:40-265
1b	AP_endonuc_2-1oadB02	B:40-265

Asymmetric Unit(hide GO term definitions)

Chain A,B (XYLA_STRRU | P24300)

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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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Glu A:186 - Pro A:187	[ RasMol ]
		Glu B:186 - Pro B:187	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1oad
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	XYLA_STRRU \| P24300
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	5.3.1.5
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	XYLA_STRRU \| P24300
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1gw9	TRI-IODIDE DERIVATIVE OF XYLOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS
1mnz	ATOMIC STRUCTURE OF GLUCOSE ISOMERASE
1o1h	STRUCTURE OF GLUCOSE ISOMERASE DERIVATIZED WITH KR.
1xib	D-XYLOSE ISOMERASE (PH 7.4)
1xic	D-XYLOSE ISOMERASE COMPLEXED WITH D-XYLOSE (PH 9.0)
1xid	D-XYLOSE ISOMERASE COMPLEXED WITH L-ASCORBIC ACID, MN, AND MG (PH 7.4)
1xie	D-XYLOSE ISOMERASE COMPLEXED WITH 1,5- DIANHYDROSORBITOL (PH 7.4)
1xif	D-XYLOSE ISOMERASE COMPLEXED WITH GLUCOSE, MN, AND MG (PH 8.0)
1xig	D-XYLOSE ISOMERASE COMPLEXED WITH XYLITOL, MG, AND MN (PH 7.4)
1xih	D-XYLOSE ISOMERASE COMPLEXED WITH D-SORBITOL AND NO ADDED MN (PH 9.0)
1xii	D-XYLOSE ISOMERASE COMPLEXED WITH 300MM D- XYLULOSE AND MN (PH 8.0)
1xij	D-XYLOSE ISOMERASE COMPLEXED WITH THREONATE AND MN (PH 9.0)
1xis	XYLOSE ISOMERASE COMPLEX WITH MNCL2
2xis	XYLOSE ISOMERASE COMPLEX WITH XYLITOL
3xis	XYLOSE ISOMERASE COMPLEX WITH XYLOSE
4xis	XYLOSE ISOMERASE COMPLEX WITH XYLOSE AND MNCL2
8xia	D-XYLOSE ISOMERASE COMPLEX WITH D-XYLOSE
9xia	D-XYLOSE ISOMERASE COMPLEX WITH INACTIVATOR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (8, 8)

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