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(-) Description

Title :  PROTEIN CRYSTALLIZATION AND MICROGRAVITY: GLUCOSE ISOMERASE CRYSTALS GROWN DURING THE PCDF-PROTEIN MISSION
 
Authors :  K. Decanniere, L. -D. Patino-Lopez, M. Sleutel, C. Evrard, C. Van De W E. Haumont, J. A. Gavira, F. Otalora, D. Maes
Date :  21 Nov 11  (Deposition) - 29 Feb 12  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Isomerase, Microgravity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Decanniere, L. -D. Patino-Lopez, M. Sleutel, C. Evrard, C. Van De Weerdt, E. Haumont, J. A. Gavira, F. Otalora, D. Maes
Protein Crystallization And Microgravity: Glucose Isomerase Crystals Grown During The Pcdf-Protein Mission
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - XYLOSE ISOMERASE
    Chains: A
    EC Number: 5.3.1.5
    Organism Scientific: STREPTOMYCES RUBIGINOSUS
    Organism Taxid: 1929
    Synonym: D-XYLOSE KETOL ISOMERASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CO2Ligand/IonCOBALT (II) ION
2GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2GOL8Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:25 , PRO A:187 , TYR A:254 , GLN A:256 , HOH A:2036 , HOH A:2037 , HOH A:2266 , HOH A:2310 , HOH A:2311 , HOH A:2312 , HOH A:2453BINDING SITE FOR RESIDUE GOL A1388
2AC2SOFTWAREHIS A:54 , TRP A:137 , GLU A:181 , ASP A:245 , ASP A:287 , CO A:1390 , HOH A:2146 , HOH A:2258 , HOH A:2303BINDING SITE FOR RESIDUE GOL A1389
3AC3SOFTWAREGLU A:181 , GLU A:217 , ASP A:245 , ASP A:287 , GOL A:1389 , HOH A:2258BINDING SITE FOR RESIDUE CO A1390
4AC4SOFTWAREGLU A:217 , HIS A:220 , ASP A:255 , ASP A:257 , HOH A:2277BINDING SITE FOR RESIDUE CO A1391

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A8N)

(-) 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 4A8N)

(-) 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 4A8N)

(-) 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: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 d4a8na_ A: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4a8n A   2 NYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGAR 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
   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)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A8N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A8N)

(-) 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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  4a8n
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  XYLA_STRRU | P24300
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  5.3.1.5
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 Related Entries

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

UniProtKB/Swiss-Prot
        XYLA_STRRU | P24300: 1gw9 1mnz 1o1h 1oad 1xib 1xic 1xid 1xie 1xif 1xig 1xih 1xii 1xij 1xis 2g4j 2glk 2gub 2gve 2xis 3cwh 3gnx 3kbj 3kbm 3kbn 3kbs 3kbv 3kbw 3kcj 3kcl 3kco 3n4a 3qys 3qza 3u3h 3xis 4a8i 4a8l 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

1gw9 TRI-IODIDE DERIVATIVE OF XYLOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS
1mnz ATOMIC STRUCTURE OF GLUCOSE ISOMERASE
1o1h STRUCTURE OF GLUCOSE ISOMERASE DERIVATIZED WITH KR.
1oad GLUCOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS IN P21212 CRYSTAL FORM
1xib D-XYLOSE ISOMERASE (PH 7.4)
1xic D-XYLOSE ISOMERASE COMPLEXED WITH D-XYLOSE (PH 9.0)
1xid D-XYLOSE ISOMERASE COMPLEXED WITH L-ASCORBIC ACID, MN , AND MG (PH 7.4)
1xie D-XYLOSE ISOMERASE COMPLEXED WITH 1,5-DIANHYDROSORBITOL (PH 7.4)
1xif D-XYLOSE ISOMERASE COMPLEXED WITH GLUCOSE, MN, AND MG (PH 8.0)
1xig D-XYLOSE ISOMERASE COMPLEXED WITH XYLITOL, MG, AND MN (PH 7.4)
1xih D-XYLOSE ISOMERASE COMPLEXED WITH D-SORBITOL AND NO ADDED MN (PH 9.0)
1xii D-XYLOSE ISOMERASE COMPLEXED WITH 300MM D-XYLULOSE AND MN (PH 8.0)
1xij D-XYLOSE ISOMERASE COMPLEXED WITH THREONATE AND MN (PH 9.0)
1xis XYLOSE ISOMERASE COMPLEX WITH MNCL2
2glk HIGH-RESOLUTION STUDY OF D-XYLOSE ISOMERASE, 0. 94ARESOLUTION.
2gub CRYSTAL STRUCTURE OF METAL FREE D-XYLOSE ISOMERASE.
2gve TIME-OF-FLIGHT NEUTRON DIFFRACTION STRUCTURE OF D- XYLOSEISOMERASE
2xis XYLOSE ISOMERASE COMPLEX WITH XYLITOL
3xis XYLOSE ISOMERASE COMPLEX WITH XYLOSE
4a8i PROTEIN CRYSTALLIZATION AND MICROGRAVITY: GLUCOSE ISOMERASE CRYSTALS GROWN DURING THE PCDF-PROTEIN MISSION
4a8l PROTEIN CRYSTALLIZATION AND MICROGRAVITY: GLUCOSE ISOMERASE CRYSTALS GROWN DURING THE PCDF-PROTEIN MISSION
4a8r PROTEIN CRYSTALLIZATION AND MICROGRAVITY: GLUCOSE ISOMERASE CRYSTALS GROWN DURING THE PCDF-PROTEIN MISSION
4xis XYLOSE ISOMERASE COMPLEX WITH XYLOSE AND MNCL2
8xia D-XYLOSE ISOMERASE COMPLEX WITH D-XYLOSE
9xia D-XYLOSE ISOMERASE COMPLEX WITH INACTIVATOR