3KBJ - JenaLib

Title :   ROOM TEMPERATURE X-RAY STRUCTURE OF APO-D-XYLOSE ISOMERASE

Authors :   A. Y. Kovalevsky, L. Hanson, P. Langan

Date :   20 Oct 09 (Deposition) - 29 Sep 10 (Release) - 31 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Apo-Form, Enzyme, Sugar Conversion, Carbohydrate Metabolism, Metal- Binding, Pentose Shunt, Xylose Metabolism, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Y. Kovalevsky, B. L. Hanson, S. A. Mason, T. Yoshida, S. Z. Fisher, M. Mustyakimov, V. T. Forsyth, M. P. Blakeley, D. A. Keen, P. Langan
Identification Of The Elusive Hydronium Ion Exchanging Role With A Proton In An Enzyme At Lower Ph Values.
Angew. Chem. Int. Ed. Engl. V. 50 7520 2011
PubMed-ID: 21604345 | Reference-DOI: 10.1002/ANIE.201101753

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

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

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

    Alignment length:388
                                    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        
           XYLA_STRRU     1 MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG 388
               SCOP domains d3kbja_ A: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------AP_endonuc_2-3kbjA01 A:40-265                                                                                                                                                                                                     --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhh.eeeehhhhh...............hhhhhhhhhhhhh..eeeeehhhhh....hhhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhh...eeee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....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
                 3kbj A   1 MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG 388
                                    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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (8, 8)

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.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3kbj)

	Sites
(no "Sites" information available for 3kbj)

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

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3kbj
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	XYLA_STRRU \| P24300
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	5.3.1.5
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

3kbm	ROOM TEMPERATURE X-RAY STRUCTURE OF D-XYLOSE ISOMERASE COMPLEXED WITH 2CD(2+) CO-FACTORS AND D12-D-ALPHA-GLUCOSE IN THE CYCLIC FORM
3kbn	ROOM TEMPERATURE STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX WITH 2NI(2+) CO-FACTORS AND D12-D-GLUCOSE IN THE LINEAR FORM
3kbs	ROOM TEMPERATURE X-RAY STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX WITH 2CD(2+) CO-FACTORS
3kbv	ROOM TEMPERATURE STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX WITH 2NI(2+) CO-FACTORS
3kbw	ROOM TEMPERATURE X-RAY MIXED-METAL STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX WITH NI(2+) AND MG(2+) CO-FACTORS
3kcj	ROOM TEMPERATURE NEUTRON STRUCTURE OF APO-D-XYLOSE ISOMERASE (REFINED JOINTLY WITH X-RAY STRUCTURE 3KBJ)
3kcl	ROOM TEMPERATURE NEUTRON STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX WITH TWO CD2+ CATIONS AND D12-D-ALPHA-GLUCOSE IN THE RING FORM (REFINED JOINTLY WITH X-RAY STRUCTURE 3KBM)
3kco	ROOM TEMPERATURE NEUTRON STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX WITH TWO NI2+ CATIONS AND D12-D-GLUCOSE IN THE LINEAR FORM (REFINED JOINTLY WITH X-RAY STRUCTURE 3KBN)

Description