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(-) Description

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

Molecule 1 - XYLOSE ISOMERASE
    ChainsA
    EC Number5.3.1.5
    EngineeredYES
    GeneXYLA
    Organism ScientificSTREPTOMYCES RUBIGINOSUS
    Organism Taxid1929
    Other DetailsTHE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3KBJ)

(-) Sites  (0, 0)

(no "Site" information available for 3KBJ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KBJ)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KBJ)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1XYLOSE_ISOMERASEPS51415 Xylose isomerase family profile.XYLA_STRRU4-383  1A:4-383
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1XYLOSE_ISOMERASEPS51415 Xylose isomerase family profile.XYLA_STRRU4-383  4A:4-383

(-) Exons   (0, 0)

(no "Exon" information available for 3KBJ)

(-) 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        

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  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)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KBJ)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) 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.

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    Glu A:186 - Pro A:187   [ RasMol ]  
 
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        XYLA_STRRU | P243001gw9 1mnz 1o1h 1oad 1xib 1xic 1xid 1xie 1xif 1xig 1xih 1xii 1xij 1xis 2g4j 2glk 2gub 2gve 2xis 3cwh 3gnx 3kbm 3kbn 3kbs 3kbv 3kbw 3kcj 3kcl 3kco 3n4a 3qys 3qza 3u3h 3xis 4a8i 4a8l 4a8n 4a8r 4duo 4dvo 4e3v 4j4k 4lnc 4qdp 4qdw 4qe1 4qe4 4qe5 4qee 4qeh 4us6 4w4q 4xis 4zb0 4zb2 4zb5 4zbc 5avh 5avn 5i7g 8xia 9xia

(-) 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)