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(-) Description

Title :  CRYSTAL STRUCTURE OF XYLOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS CRYOPROTECTED IN PROLINE
 
Authors :  J. J. Tanner, T. A. Pemberton
Date :  10 Mar 12  (Deposition) - 25 Jul 12  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Pemberton, B. R. Still, E. M. Christensen, H. Singh, D. Srivastava, J. J. Tanner
Proline: Mother Nature'S Cryoprotectant Applied To Protein Crystallography.
Acta Crystallogr. , Sect. D V. 68 1010 2012
PubMed-ID: 22868767  |  Reference-DOI: 10.1107/S0907444912019580

(-) Compounds

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

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MN1Ligand/IonMANGANESE (II) ION
3PRO1Mod. Amino AcidPROLINE
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MN-1Ligand/IonMANGANESE (II) ION
3PRO4Mod. Amino AcidPROLINE
4SO48Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:278 , GLY A:279 , TYR A:280 , SER A:281 , HOH A:519BINDING SITE FOR RESIDUE PRO A 401
2AC2SOFTWARETRP A:20 , GLN A:21 , GLY A:22 , ARG A:23 , HOH A:742 , HOH A:745BINDING SITE FOR RESIDUE SO4 A 402
3AC3SOFTWAREARG A:23 , ASP A:28 , ALA A:29 , HOH A:578BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWAREGLU A:181 , GLU A:217 , ASP A:245 , ASP A:287 , HOH A:808 , HOH A:810BINDING SITE FOR RESIDUE MG A 404
5AC5SOFTWAREGLU A:217 , HIS A:220 , ASP A:255 , ASP A:257 , HOH A:806BINDING SITE FOR RESIDUE MN A 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E3V)

(-) 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 4E3V)

(-) 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 4E3V)

(-) 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:387
                                                                                                                                                                                                                                                                                                                                                                                                                           388 
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382     | 
           XYLA_STRRU     3 YQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG-   -
               SCOP domains d4e3va_ 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
                 4e3v A   3 YQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGAR-P 401
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382    | |
                                                                                                                                                                                                                                                                                                                                                                                                                          387 |
                                                                                                                                                                                                                                                                                                                                                                                                                            401
   Legend:   → Mismatch (orange background)
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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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E3V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E3V)

(-) 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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 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 4a8n 4a8r 4duo 4dvo 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

4e3u 4e3w 4e3x