1MNZ - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   ATOMIC STRUCTURE OF GLUCOSE ISOMERASE

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

Date :   06 Sep 02 (Deposition) - 25 Sep 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.99

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   High Resolution, Alpha/Beta Barrel, Gi Fold, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Nowak, S. Panjikar, P. A. Tucker
Atomic Structure Of Glucose Isomerase
To Be Published
PubMed: search

Molecule 1 - XYLOSE ISOMERASE
	Chains	:	A
	EC Number	:	5.3.1.5
	Engineered	:	YES
	Other Details	:	THE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN STREPTOMYCES RUBIGINOUS.
	Synthetic	:	YES

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 4)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	MRD	1	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MRD	4	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
4	TRS	4	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:181 , GLU A:217 , ASP A:245 , ASP A:287 , TRS A:392	BINDING SITE FOR RESIDUE MG A 389
2	AC2	SOFTWARE	GLU A:217 , HIS A:220 , ASP A:255 , ASP A:257 , HOH A:1024	BINDING SITE FOR RESIDUE CA A 390
3	AC3	SOFTWARE	TRP A:16 , HIS A:54 , TRP A:137 , GLU A:181 , GLU A:217 , HIS A:220 , ASP A:245 , ASP A:287 , MG A:389 , HOH A:1050 , HOH A:1071 , HOH A:1146	BINDING SITE FOR RESIDUE TRS A 392
4	AC4	SOFTWARE	TRP A:16 , PRO A:25 , HIS A:54 , THR A:95 , HOH A:1077 , HOH A:1098	BINDING SITE FOR RESIDUE MRD A 391

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

Asymmetric Unit

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

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

Asymmetric Unit (1, 1)

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

(no "Exon" information available for 1MNZ)

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 d1mnza_ A: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1mnzA00 A:2-388 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.eeeehhhhh...............hhhhhhhhhhhh...eeeeehhhhh....hhhhhhhhhhhhhhhhhhhh....eee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhh...eeee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...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: A:4-383 UniProt: 4-383                                                                                                                                                                                                                                                                                                                                               ----- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mnz A   2 NYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG 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

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)

d1mnza_

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)

[unclassified] (4)

1mnzA00

A:2-388

(no "Pfam Domain" information available for 1MNZ)

Asymmetric Unit(hide GO term definitions)

Chain A (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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		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu A:186 - Pro A:187	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	1mnz
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
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	XYLA_STRRU \| P24300
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
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	5.3.1.5
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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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1xib	THE SAME PROTEIN BUT AT 1.60 A RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

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