1O1H - JenaLib

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Title :   STRUCTURE OF GLUCOSE ISOMERASE DERIVATIZED WITH KR.

Authors :   E. Nowak, S. Panjikar, P. A. Tucker

Date :   07 Nov 02 (Deposition) - 27 Nov 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Kr Derivatization. , Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Nowak, S. Panjikar, P. A. Tucker
Structure Of Glucose Isomerase Derivatized With Kr.
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - XYLOSE ISOMERASE
	Chains	:	A, B
	EC Number	:	5.3.1.5
	Organism Scientific	:	STREPTOMYCES RUBIGINOSUS
	Organism Taxid	:	1929
	Other Details	:	THE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH. THEY HAVE PURIFIED IT FROM STREPTOMYCES RUBIGINOSUS.

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 16)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	CL	4	Ligand/Ion	CHLORIDE ION
3	KR	4	Ligand/Ion	KRYPTON
4	MG	2	Ligand/Ion	MAGNESIUM ION
5	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
6	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	KR	-1	Ligand/Ion	KRYPTON
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
6	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	KR	-1	Ligand/Ion	KRYPTON
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	MPD	4	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
6	TRS	4	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:216 , HIS A:219 , ASP A:254 , ASP A:256 , HOH A:1058	BINDING SITE FOR RESIDUE CA A 1001
02	AC2	SOFTWARE	GLU B:216 , HIS B:219 , ASP B:254 , ASP B:256 , HOH B:1453	BINDING SITE FOR RESIDUE CA B 1002
03	AC3	SOFTWARE	GLU A:180 , GLU A:216 , ASP A:244 , ASP A:286 , TRS A:1013	BINDING SITE FOR RESIDUE MG A 1003
04	AC4	SOFTWARE	GLU B:180 , GLU B:216 , ASP B:244 , ASP B:286 , TRS B:1014	BINDING SITE FOR RESIDUE MG B 1004
05	AC5	SOFTWARE	THR B:29 , GLU B:293 , HOH B:1187	BINDING SITE FOR RESIDUE CL B 1009
06	AC6	SOFTWARE	THR A:29 , GLU A:293 , HOH A:1256	BINDING SITE FOR RESIDUE CL A 1010
07	AC7	SOFTWARE	ARG B:265 , PHE B:268 , ALA B:378 , MET B:379	BINDING SITE FOR RESIDUE CL B 1011
08	AC8	SOFTWARE	ARG A:265 , PHE A:268 , ALA A:378 , MET A:379	BINDING SITE FOR RESIDUE CL A 1012
09	AC9	SOFTWARE	ALA B:135 , LEU B:164	BINDING SITE FOR RESIDUE KR B 1005
10	BC1	SOFTWARE	ALA A:135 , LEU A:164	BINDING SITE FOR RESIDUE KR A 1006
11	BC2	SOFTWARE	GLN A:233 , ARG B:204	BINDING SITE FOR RESIDUE KR B 1007
12	BC3	SOFTWARE	ALA A:200 , ARG A:204 , GLN B:233	BINDING SITE FOR RESIDUE KR A 1008
13	BC4	SOFTWARE	TRP A:15 , HIS A:53 , TRP A:136 , GLU A:180 , GLU A:216 , HIS A:219 , ASP A:244 , ASP A:286 , MG A:1003 , HOH A:1058 , HOH A:1091 , HOH A:1209	BINDING SITE FOR RESIDUE TRS A 1013
14	BC5	SOFTWARE	TRP B:15 , HIS B:53 , TRP B:136 , GLU B:180 , GLU B:216 , HIS B:219 , ASP B:244 , ASP B:286 , MG B:1004 , HOH B:1089 , HOH B:1232 , HOH B:1426 , HOH B:1453	BINDING SITE FOR RESIDUE TRS B 1014
15	BC6	SOFTWARE	PHE A:93 , THR A:94 , HOH A:1220 , HOH A:1233 , HOH A:1373	BINDING SITE FOR RESIDUE MPD A 1015
16	BC7	SOFTWARE	PHE A:25 , TRP B:15 , TRP B:19 , HIS B:53 , HOH B:1167 , HOH B:1232 , HOH B:1242 , HOH B:1442 , HOH B:1452 , HOH B:1479	BINDING SITE FOR RESIDUE MPD B 1016

(no "SS Bond" information available for 1O1H)

(no "Cis Peptide Bond" information available for 1O1H)

(no "SAP(SNP)/Variant" information available for 1O1H)

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:3-382 B:3-382

Biological Unit 1 (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:3-382 B:3-382

Biological Unit 2 (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:3-382 B:3-382

(no "Exon" information available for 1O1H)

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: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 d1o1ha_ A: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1o1hA00 A:1-386 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.eeeehhhhh...............hhhhhhhhhhhh...eeeeehhhhh....hhhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..eeee.....ee......hhhhhhhhhhhhhhhhhhhhhhhh...eeee.........ee...hhhhhhhhhh...hhh.eee..hhhhhhh...hhhhhhhhhhhh......ee.................hhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --XYLOSE_ISOMERASE  PDB: A:3-382 UniProt: 4-383                                                                                                                                                                                                                                                                                                                                               ---- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o1h A   1 NYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGAR 386
                                    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

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 d1o1hb_ B: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1o1hB00 B:1-386 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                        CATH domains
           Pfam domains (1) --------------------------------------AP_endonuc_2-1o1hB01 B:39-264                                                                                                                                                                                                     -------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------AP_endonuc_2-1o1hB02 B:39-264                                                                                                                                                                                                     -------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhh.eeeehhhhh...............hhhhhhhhhhhh...eeeeehhhhh....hhhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..eeee.....ee......hhhhhhhhhhhhhhhhhhhhhhhh...eeee.........ee...hhhhhhhhhh...hhh.eee..hhhhhhh...hhhhhhhhhhhh......ee.................hhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --XYLOSE_ISOMERASE  PDB: B:3-382 UniProt: 4-383                                                                                                                                                                                                                                                                                                                                               ---- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o1h B   1 NYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGAR 386
                                    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

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	d1o1ha_	A:
1b	d1o1hb_	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. (9)

1a	1o1hA00	A:1-386
1b	1o1hB00	B:1-386

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: AP_endonuc_2 (72)

Streptomyces rubiginosus (22)

1a	AP_endonuc_2-1o1hB01	B:39-264
1b	AP_endonuc_2-1o1hB02	B:39-264

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1o1h)

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	1o1h
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (6, 16)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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