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(-) Description

Title :  STRUCTURE DETERMINATION OF GLUCOSE ISOMERASE FROM STREPTOMYCES MURINUS AT 2.6 ANGSTROMS RESOLUTION
 
Authors :  H. Rasmussen, T. La Cour, J. Nyborg, M. Schulein
Date :  30 Sep 93  (Deposition) - 31 Jan 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Isomerase(Intramolecular Oxidoreductase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Rasmussen, T. La Cour, J. Nyborg, M. Schulein
Structure Determination Of Glucose Isomerase From Streptomyces Murinus At 2. 6 A Resolution.
Acta Crystallogr. , Sect. D V. 50 124 1994
PubMed-ID: 15299450  |  Reference-DOI: 10.1107/S0907444993009540

(-) Compounds

Molecule 1 - D-XYLOSE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.5
    Engineered: YES
    Organism Scientific: STREPTOMYCES MURINUS
    Organism Taxid: 33900

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:181 , GLU A:217 , ASP A:245 , ASP A:287 , HOH A:391BINDING SITE FOR RESIDUE MG A 389
2AC2SOFTWAREGLU A:217 , HIS A:220 , ASN A:247 , ASP A:255 , ASP A:257 , HOH A:392BINDING SITE FOR RESIDUE MG A 390
3AC3SOFTWAREGLU B:181 , GLU B:217 , ASP B:245 , ASP B:287 , HOH B:391BINDING SITE FOR RESIDUE MG B 389
4AC4SOFTWAREGLU B:217 , HIS B:220 , ASP B:255 , ASP B:257 , HOH B:392BINDING SITE FOR RESIDUE MG B 390
5CAAAUTHORGLU A:181 , GLU A:217 , HIS A:220 , ASP A:245 , ASP A:255 , ASP A:257 , ASP A:287CATALYTIC SITE IN CHAIN A
6CABAUTHORGLU B:181 , GLU B:217 , HIS B:220 , ASP B:245 , ASP B:255 , ASP B:257 , ASP B:287CATALYTIC SITE IN CHAIN B

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:186 -Pro A:187
2Glu B:186 -Pro B:187

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1XYLOSE_ISOMERASEPS51415 Xylose isomerase family profile.XYLA_STRMR4-383
 		  2A:4-383
B:4-383
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1XYLOSE_ISOMERASEPS51415 Xylose isomerase family profile.XYLA_STRMR4-383
 		  4A:4-383
B:4-383

(-) Exons   (0, 0)

(no "Exon" information available for 1DXI)

(-) 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_STRMR | P37031 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_STRMR     1 MSFQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAYGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIGNIDLAAELGAKTYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTAQGYDLRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGAGDLRAAFWLVDLLETAGYEGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKDRAAAFRADPEVQEALRAARLDQLAQPTAADGLDALLADRAAFEDFDVDAAAARGMAFEHLDQLAMDHLLGARG 388
               SCOP domains d1dxia_ A: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1dxiA00 A:1-388 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee.....................hhhhhhhhhhh...eeeeehhhh......hhhhhhhhhhhhhhhhh..eeeeeeee.....hhh.........hhhhhhhhhhhhhhhhhhhhh...eeeeee............hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee...........hhhhhhhhhh........eeeehhhhhhh...hhhhhhhhhhh....eeeeeee...............hhhhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhh......................hhhhhh....hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---XYLOSE_ISOMERASE  PDB: A:4-383 UniProt: 4-383                                                                                                                                                                                                                                                                                                                                               ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dxi A   1 MSFQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAYGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIGNIDLAAELGAKTYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTAQGYDLRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGAGDLRAAFWLVDLLETAGYEGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKDRAAAFRADPEVQEALRAARLDQLAQPTAADGLDALLADRAAFEDFDVDAAAARGMAFEHLDQLAMDHLLGARG 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        


Chain B from PDB  Type:PROTEIN  Length:388
 aligned with XYLA_STRMR | P37031 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_STRMR     1 MSFQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAYGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIGNIDLAAELGAKTYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTAQGYDLRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGAGDLRAAFWLVDLLETAGYEGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKDRAAAFRADPEVQEALRAARLDQLAQPTAADGLDALLADRAAFEDFDVDAAAARGMAFEHLDQLAMDHLLGARG 388
               SCOP domains d1dxib_ B: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1dxiB00 B:1-388 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee.....................hhhhhhhhhhh...eeeeehhhh......hhhhhhhhhhhhhhhhh..eeeeeeee.....hhh.........hhhhhhhhhhhhhhhhhhhhh...eeeeee............hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee...........hhhhhhhhhh........eeeehhhhhhh...hhhhhhhhhhh....eeeeeee...............hhhhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhh......................hhhhhh....hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---XYLOSE_ISOMERASE  PDB: B:4-383 UniProt: 4-383                                                                                                                                                                                                                                                                                                                                               ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dxi B   1 MSFQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAYGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIGNIDLAAELGAKTYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTAQGYDLRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGAGDLRAAFWLVDLLETAGYEGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKDRAAAFRADPEVQEALRAARLDQLAQPTAADGLDALLADRAAFEDFDVDAAAARGMAFEHLDQLAMDHLLGARG 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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (XYLA_STRMR | P37031)
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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