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(-) Description

Title :  THE ROLE OF THE DIVALENT METAL ION IN SUGAR BINDING, RING OPENING, AND ISOMERIZATION BY D-XYLOSE ISOMERASE: REPLACEMENT OF A CATALYTIC METAL BY AN AMINO-ACID
 
Authors :  K. N. Allen, A. Lavie, G. A. Petsko, D. Ringe
Date :  07 Dec 93  (Deposition) - 31 May 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Isomerase(Intramolecular Oxidoreductase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. N. Allen, A. Lavie, A. Glasfeld, T. N. Tanada, D. P. Gerrity, S. C. Carlson, G. K. Farber, G. A. Petsko, D. Ringe
Role Of The Divalent Metal Ion In Sugar Binding, Ring Opening, And Isomerization By D-Xylose Isomerase: Replacement Of A Catalytic Metal By An Amino Acid.
Biochemistry V. 33 1488 1994
PubMed-ID: 7906142  |  Reference-DOI: 10.1021/BI00172A027
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - XYLOSE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.5
    Engineered: YES
    Organism Scientific: STREPTOMYCES OLIVOCHROMOGENES
    Organism Taxid: 1963

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1GLO2Ligand/IonD-GLUCOSE IN LINEAR FORM
2MG2Ligand/IonMAGNESIUM ION
3OH2Ligand/IonHYDROXIDE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1GLO4Ligand/IonD-GLUCOSE IN LINEAR FORM
2MG-1Ligand/IonMAGNESIUM ION
3OH-1Ligand/IonHYDROXIDE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:53 , THR A:89 , PHE A:93 , VAL A:134 , TRP A:136 , LYS A:180 , LYS A:182 , GLU A:216 , HIS A:219 , ASP A:254 , ASP A:286 , HOH A:1263 , HOH A:1268 , OH A:1700 , PHE B:525BINDING SITE FOR RESIDUE GLO A 950
02AC2SOFTWAREPHE A:25 , HIS B:553 , THR B:589 , PHE B:593 , VAL B:634 , TRP B:636 , LYS B:680 , LYS B:682 , GLU B:716 , HIS B:719 , ASP B:754 , ASP B:786 , MG B:901 , HOH B:1345 , OH B:1800BINDING SITE FOR RESIDUE GLO B 960
03AC3SOFTWAREGLU A:216 , HIS A:219 , ASP A:254 , ASP A:256 , OH A:1700BINDING SITE FOR RESIDUE MG A 401
04AC4SOFTWAREGLU A:216 , HIS A:219 , ASP A:254 , ASP A:256 , MG A:401 , GLO A:950BINDING SITE FOR RESIDUE OH A 1700
05AC5SOFTWAREGLU B:716 , HIS B:719 , ASP B:754 , ASP B:756 , GLO B:960 , OH B:1800BINDING SITE FOR RESIDUE MG B 901
06AC6SOFTWAREGLU B:716 , ASP B:754 , ASP B:756 , MG B:901 , GLO B:960BINDING SITE FOR RESIDUE OH B 1800
07M1AAUTHORLYS A:180 , ASP A:244 , ASP A:286 , GLU A:216 , GLO A:950WHILE THE ACTIVE SITE IN THE WILD TYPE ENZYME CONTAINS THE METAL BINDING SITE, IN THIS MUTANT THE METAL IONS IN THESE SITES ARE REPLACED BY THE N-EPSILON AMINO GROUPS OF LYS
08M1BAUTHORLYS B:680 , ASP B:744 , ASP B:786 , GLU B:716 , GLO B:960WHILE THE ACTIVE SITE IN THE WILD TYPE ENZYME CONTAINS THE METAL BINDING SITE, IN THIS MUTANT THE METAL IONS IN THESE SITES ARE REPLACED BY THE N-EPSILON AMINO GROUPS OF LYS
09M2AAUTHORMG A:401 , GLU A:216 , HIS A:219 , ASP A:254 , ASP A:256 , OH A:1700METAL BINDING SITE
10M2BAUTHORMG B:901 , GLU B:716 , HIS B:719 , ASP B:754 , ASP B:756 , OH B:1800METAL BINDING SITE

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:185 -Pro A:186
2Glu B:685 -Pro B:686

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1XYLOSE_ISOMERASEPS51415 Xylose isomerase family profile.XYLA_STROL4-383
 		  2A:3-382
B:503-882
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1XYLOSE_ISOMERASEPS51415 Xylose isomerase family profile.XYLA_STROL4-383
 		  4A:3-382
B:503-882

(-) Exons   (0, 0)

(no "Exon" information available for 1XYM)

(-) 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_STROL | P15587 from UniProtKB/Swiss-Prot  Length:387

    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_STROL     2 SYQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAHGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAKTYVAWGGREGAESGAAKDVRVALDRMKEAFDLLGEYVTSQGYDTRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGAGDLRAAFWLVDLLESAGYEGPRHFDFKPPRTEDIDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELAQPTAADGVQELLADRTAFEDFDVDAAAARGMAFERLDQLAMDHLLGAR 387
               SCOP domains d1xyma_ A: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1xymA00 A:1-386 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeehhhhhh...............hhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhhhhhhhhhhhh...eeeeeee.eeee......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...........hhhhhhhhhh......eeeeeehhhhhhh...hhhhhhhhhhh...eeeeee..................hhhhhhhhhhhh.eeee.eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhh.......hhhhhhh........hhhhhh....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --XYLOSE_ISOMERASE  PDB: A:3-382 UniProt: 4-383                                                                                                                                                                                                                                                                                                                                               ---- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xym A   1 SYQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAHGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAKTYVAWGGREGAESGAAKDVRVALDRMKEAFDLLGEYVTSQGYDTRFAIKPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGAGDLRAAFWLVDLLESAGYEGPRHFDFKPPRTEDIDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELAQPTAADGVQELLADRTAFEDFDVDAAAARGMAFERLDQLAMDHLLGAR 386
                                    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:386
 aligned with XYLA_STROL | P15587 from UniProtKB/Swiss-Prot  Length:387

    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_STROL     2 SYQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAHGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAKTYVAWGGREGAESGAAKDVRVALDRMKEAFDLLGEYVTSQGYDTRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGAGDLRAAFWLVDLLESAGYEGPRHFDFKPPRTEDIDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELAQPTAADGVQELLADRTAFEDFDVDAAAARGMAFERLDQLAMDHLLGAR 387
               SCOP domains d1xymb_ B: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1xymB00 B:501-886 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) --------------------------------------AP_endonuc_2-1xymB01 B:539-764                                                                                                                                                                                                    -------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------AP_endonuc_2-1xymB02 B:539-764                                                                                                                                                                                                    -------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .........eeeehhhhhh...............hhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhh..eeeeeee.................hhhhhhhhhhhhhhhhhhhhh...eeeeeee.eeee......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...........hhhhhhhhhh......eeeeeehhhhhhh...hhhhhhhhhhh...eeeeee..................hhhhhhhhhhhh.eeee.eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhh.......hhhhhhh........hhhhhh....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --XYLOSE_ISOMERASE  PDB: B:503-882 UniProt: 4-383                                                                                                                                                                                                                                                                                                                                             ---- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xym B 501 SYQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAHGVTFHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAKTYVAWGGREGAESGAAKDVRVALDRMKEAFDLLGEYVTSQGYDTRFAIKPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGIKYDQDLRFGAGDLRAAFWLVDLLESAGYEGPRHFDFKPPRTEDIDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELAQPTAADGVQELLADRTAFEDFDVDAAAARGMAFERLDQLAMDHLLGAR 886
                                   510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880
   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  (1, 2)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (XYLA_STROL | P15587)
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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  1xym
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  XYLA_STROL | P15587
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 Related Entries

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

UniProtKB/Swiss-Prot
        XYLA_STROL | P15587: 1muw 1s5m 1s5n 1xya 1xyb 1xyc 1xyl 2gyi

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1XYM)