1XYB - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Title :   X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSIS

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

Date :   03 Jan 94 (Deposition) - 31 May 94 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.96

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

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

Reference :   A. Lavie, K. N. Allen, G. A. Petsko, D. Ringe
X-Ray Crystallographic Structures Of D-Xylose Isomerase-Substrate Complexes Position The Substrate And Provide Evidence For Metal Movement During Catalysis.
Biochemistry V. 33 5469 1994
PubMed-ID: 8180169 | Reference-DOI: 10.1021/BI00184A016
(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	GLO	2	Ligand/Ion	D-GLUCOSE IN LINEAR FORM
2	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	GLO	4	Ligand/Ion	D-GLUCOSE IN LINEAR FORM
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:53 , THR A:89 , PHE A:93 , VAL A:134 , TRP A:136 , GLU A:180 , LYS A:182 , GLU A:216 , HIS A:219 , ASP A:254 , ASP A:286 , MG A:400 , MG A:401 , HOH A:1292 , HOH A:1700 , PHE B:525	BINDING SITE FOR RESIDUE GLO A 950
02	AC2	SOFTWARE	PHE A:25 , HIS B:553 , THR B:589 , PHE B:593 , VAL B:634 , TRP B:636 , GLU B:680 , LYS B:682 , GLU B:716 , HIS B:719 , ASP B:754 , ASP B:786 , MG B:900 , MG B:901 , HOH B:1146 , HOH B:1149 , HOH B:1800	BINDING SITE FOR RESIDUE GLO B 960
03	AC3	SOFTWARE	GLU A:180 , GLU A:216 , ASP A:244 , ASP A:286 , GLO A:950	BINDING SITE FOR RESIDUE MG A 400
04	AC4	SOFTWARE	GLU A:216 , HIS A:219 , ASP A:254 , ASP A:256 , GLO A:950 , HOH A:1700	BINDING SITE FOR RESIDUE MG A 401
05	AC5	SOFTWARE	GLU B:680 , GLU B:716 , ASP B:744 , ASP B:786 , GLO B:960	BINDING SITE FOR RESIDUE MG B 900
06	AC6	SOFTWARE	GLU B:716 , HIS B:719 , ASP B:754 , ASP B:756 , GLO B:960 , HOH B:1800	BINDING SITE FOR RESIDUE MG B 901
07	M1A	AUTHOR	MG A:400 , GLU A:180 , ASP A:244 , ASP A:286 , GLU A:216	METAL BINDING SITE
08	M1B	AUTHOR	MG B:900 , GLU B:680 , ASP B:744 , ASP B:786 , GLU B:716	METAL BINDING SITE
09	M2A	AUTHOR	MG A:401 , GLU A:216 , HIS A:219 , ASP A:254 , ASP A:256 , HOH A:1700	METAL BINDING SITE
10	M2B	AUTHOR	MG B:901 , GLU B:716 , HIS B:719 , ASP B:754 , ASP B:756 , HOH B:1800	METAL BINDING SITE

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

Asymmetric Unit

No.	Residues
1	Glu A:185	-	Pro A:186
2	Glu B:685	-	Pro B:686

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

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:503-882

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:503-882

(no "Exon" information available for 1XYB)

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_STROL | P15587 from UniProtKB/Swiss-Prot  Length:387

    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_STROL     2 SYQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAHGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAKTYVAWGGREGAESGAAKDVRVALDRMKEAFDLLGEYVTSQGYDTRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGAGDLRAAFWLVDLLESAGYEGPRHFDFKPPRTEDIDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELAQPTAADGVQELLADRTAFEDFDVDAAAARGMAFERLDQLAMDHLLGAR 387
               SCOP domains d1xyba_ A: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1xybA00 A:1-386 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeehhhhhh...............hhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhhhhhhhhhhhh...eeeeeee.eeee......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...........hhhhhhhhhh......eeeeeehhhhhhh...hhhhhhhhhhh...eeeeee..................hhhhhhhhhhhh.eeee.eeee........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
                 1xyb A   1 SYQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAHGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAKTYVAWGGREGAESGAAKDVRVALDRMKEAFDLLGEYVTSQGYDTRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGAGDLRAAFWLVDLLESAGYEGPRHFDFKPPRTEDIDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELAQPTAADGVQELLADRTAFEDFDVDAAAARGMAFERLDQLAMDHLLGAR 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_STROL | P15587 from UniProtKB/Swiss-Prot  Length:387

    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_STROL     2 SYQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAHGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAKTYVAWGGREGAESGAAKDVRVALDRMKEAFDLLGEYVTSQGYDTRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGAGDLRAAFWLVDLLESAGYEGPRHFDFKPPRTEDIDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELAQPTAADGVQELLADRTAFEDFDVDAAAARGMAFERLDQLAMDHLLGAR 387
               SCOP domains d1xybb_ B: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1xybB00 B:501-886 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) --------------------------------------AP_endonuc_2-1xybB01 B:539-764                                                                                                                                                                                                    -------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------AP_endonuc_2-1xybB02 B:539-764                                                                                                                                                                                                    -------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .........eeeehhhhhh...............hhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhhhhhhhhhhhh...eeeeeee.eeee......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...........hhhhhhhhhh......eeeeeehhhhhhh...hhhhhhhhhhh...eeeeee..................hhhhhhhhhhhh.eeee.eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhh.......hhhhhhh........hhhhhh....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --XYLOSE_ISOMERASE  PDB: B:503-882 UniProt: 4-383                                                                                                                                                                                                                                                                                                                                             ---- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xyb B 501 SYQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAHGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAKTYVAWGGREGAESGAAKDVRVALDRMKEAFDLLGEYVTSQGYDTRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGAGDLRAAFWLVDLLESAGYEGPRHFDFKPPRTEDIDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELAQPTAADGVQELLADRTAFEDFDVDAAAARGMAFERLDQLAMDHLLGAR 886
                                   510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880

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 olivochromogenes [TaxId: 1963] (9)

1a	d1xyba_	A:
1b	d1xybb_	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 olivochromogenes. Organism_taxid: 1963 (6)

1a	1xybA00	A:1-386
1b	1xybB00	B:501-886

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: AP_endonuc_2 (72)

Streptomyces olivochromogenes (8)

1a	AP_endonuc_2-1xybB01	B:539-764
1b	AP_endonuc_2-1xybB02	B:539-764

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:685 - Pro B:686	[ RasMol ]

Biological Unit
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	1xyb
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	XYLA_STROL \| P15587
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	XYLA_STROL \| P15587
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UniProtKB/Swiss-Prot
	XYLA_STROL \| P15587	:	1muw 1s5m 1s5n 1xya 1xyc 1xyl 1xym 2gyi

(no "Related Entries Specified in the PDB File" available for 1XYB)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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Exons (0, 0)

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