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(-) Description

Title :  PROTEIN ENGINEERING OF XYLOSE (GLUCOSE) ISOMERASE FROM ACTINOPLANES MISSOURIENSIS. 1. CRYSTALLOGRAPHY AND SITE-DIRECTED MUTAGENESIS OF METAL BINDING SITES
 
Authors :  J. Janin
Date :  06 Apr 92  (Deposition) - 15 Jul 93  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Isomerase(Intramolecular Oxidoreductse) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jenkins, J. Janin, F. Rey, M. Chiadmi, H. Van Tilbeurgh, I. Lasters, M. De Maeyer, D. Van Belle, S. J. Wodak, M. Lauwereys, P. Stanssens, G. Matthyssens, A. M. Lambeir
Protein Engineering Of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography And Site-Directed Mutagenesis Of Metal Binding Sites.
Biochemistry V. 31 5449 1992
PubMed-ID: 1610791  |  Reference-DOI: 10.1021/BI00139A005
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-XYLOSE ISOMERASE
    Chains: A, B, C, D
    EC Number: 5.3.1.5
    Engineered: YES
    Organism Scientific: ACTINOPLANES MISSOURIENSIS
    Organism Taxid: 1866

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
2XLS4Ligand/IonD-XYLOSE (LINEAR FORM)

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:16 , HIS A:54 , TRP A:137 , GLU A:181 , LYS A:183 , GLU A:217 , HIS A:220 , ASP A:245 , ASP A:292 , MG A:395 , HOH A:454 , HOH A:455 , HOH A:539BINDING SITE FOR RESIDUE XLS A 397
2AC2SOFTWARETRP B:16 , HIS B:54 , TRP B:137 , GLU B:181 , LYS B:183 , GLU B:217 , HIS B:220 , ASP B:245 , ASP B:292 , MG B:395 , HOH B:458 , HOH B:459BINDING SITE FOR RESIDUE XLS B 397
3AC3SOFTWARETRP C:16 , HIS C:54 , PHE C:94 , TRP C:137 , GLU C:181 , GLU C:217 , HIS C:220 , ASP C:245 , ASP C:292 , MG C:395 , HOH C:467 , HOH C:468 , HOH C:622BINDING SITE FOR RESIDUE XLS C 397
4AC4SOFTWARETRP D:16 , HIS D:54 , TRP D:137 , GLU D:181 , LYS D:183 , GLU D:217 , HIS D:220 , ASP D:245 , ASP D:292 , MG D:395 , HOH D:469 , HOH D:470 , HOH D:549BINDING SITE FOR RESIDUE XLS D 397
5AC5SOFTWAREGLU A:181 , GLU A:217 , ASP A:245 , ASP A:292 , XLS A:397BINDING SITE FOR RESIDUE MG A 395
6AC6SOFTWAREGLU B:181 , GLU B:217 , ASP B:245 , ASP B:292 , XLS B:397BINDING SITE FOR RESIDUE MG B 395
7AC7SOFTWAREGLU C:181 , GLU C:217 , ASP C:245 , ASP C:292 , XLS C:397BINDING SITE FOR RESIDUE MG C 395
8AC8SOFTWAREGLU D:181 , GLU D:217 , ASP D:245 , ASP D:292 , XLS D:397BINDING SITE FOR RESIDUE MG D 395

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5XIN)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:186 -Pro A:187
2Glu B:186 -Pro B:187
3Glu C:186 -Pro C:187
4Glu D:186 -Pro D:187

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5XIN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5XIN)

(-) Exons   (0, 0)

(no "Exon" information available for 5XIN)

(-) Sequences/Alignments

Asymmetric/Biological 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:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d5xina_ A: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 5xinA00 A:3-394 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eeeehhhhh...............hhhhhhhhhhhhh..eee.hhhhhh....hhhhhhhhhhhhhhhhhhhh....eee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..eeeee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........ee...hhhhhhhhhh...hhh.eee..hhhhhhh...hhhhhhhhhhhhh.....ee.................hhhhhhhhhhhhhhhhhhh......eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xin A   3 VQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIGAYGITFHDDDLVPFGSDAQTRDGIIAGFKKALDETGLIVPMVTTNLFTHPVFKDGGFTSNDRSVRRYAIRKVLRQMDLGAELGAKTLVLWGGREGAEYDSAKDVSAALDRYREALNLLAQYSEDRGYGLRFAIEPKPNEPRGDILLPTAGHAIAFVQELERPELFGINPETGHEQMSNLNFTQGIAQALWHKKLFHIDLNGQHGPKFAQDLVFGHGDLLNAFSLVDLLENGPDGAPAYDGPRHFDYKPSRTEDYDGVWESAKANIRMYLLLKERAKAFRADPEVQEALAASKVAELKTPTLNPGEGYAELLADRSAFEDYDADAVGAKGFGFVKLNQLAIEHLLGAR 394
                                    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       392  


Chain B from PDB  Type:PROTEIN  Length:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d5xinb_ B: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 5xinB00 B:3-394 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eeeehhhhh...............hhhhhhhhhhhhh..eee.hhhhhh....hhhhhhhhhhhhhhhhhhhh....eee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..eeeee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee...hhhhhhhhhh...hhh.eee..hhhhhhh...hhhhhhhhhhhhh....eee.................hhhhhhhhhhhhhh...........eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xin B   3 VQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIGAYGITFHDDDLVPFGSDAQTRDGIIAGFKKALDETGLIVPMVTTNLFTHPVFKDGGFTSNDRSVRRYAIRKVLRQMDLGAELGAKTLVLWGGREGAEYDSAKDVSAALDRYREALNLLAQYSEDRGYGLRFAIEPKPNEPRGDILLPTAGHAIAFVQELERPELFGINPETGHEQMSNLNFTQGIAQALWHKKLFHIDLNGQHGPKFAQDLVFGHGDLLNAFSLVDLLENGPDGAPAYDGPRHFDYKPSRTEDYDGVWESAKANIRMYLLLKERAKAFRADPEVQEALAASKVAELKTPTLNPGEGYAELLADRSAFEDYDADAVGAKGFGFVKLNQLAIEHLLGAR 394
                                    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       392  


Chain C from PDB  Type:PROTEIN  Length:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d5xinc_ C: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 5xinC00 C:3-394 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eeeehhhhh...............hhhhhhhhhhhhh..eee.hhhhhh....hhhhhhhhhhhhhhhhhhhh....eee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..eeeee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee...hhhhhhhhhh...hhh.eee..hhhhhhh...hhhhhhhhhhhh......ee.................hhhhhhhhhhhhhh...........eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xin C   3 VQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIGAYGITFHDDDLVPFGSDAQTRDGIIAGFKKALDETGLIVPMVTTNLFTHPVFKDGGFTSNDRSVRRYAIRKVLRQMDLGAELGAKTLVLWGGREGAEYDSAKDVSAALDRYREALNLLAQYSEDRGYGLRFAIEPKPNEPRGDILLPTAGHAIAFVQELERPELFGINPETGHEQMSNLNFTQGIAQALWHKKLFHIDLNGQHGPKFAQDLVFGHGDLLNAFSLVDLLENGPDGAPAYDGPRHFDYKPSRTEDYDGVWESAKANIRMYLLLKERAKAFRADPEVQEALAASKVAELKTPTLNPGEGYAELLADRSAFEDYDADAVGAKGFGFVKLNQLAIEHLLGAR 394
                                    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       392  


Chain D from PDB  Type:PROTEIN  Length:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d5xind_ D: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 5xinD00 D:3-394 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eeeehhhhh...............hhhhhhhhhhhhh..eee.hhhhhh....hhhhhhhhhhhhhhhhhhhh....eee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..eeee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.........ee...hhhhhhhhhh...hhh.eee..hhhhhhh...hhhhhhhhhhhhh.....ee.................hhhhhhhhhhhhhh...........eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xin D   3 VQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIGAYGITFHDDDLVPFGSDAQTRDGIIAGFKKALDETGLIVPMVTTNLFTHPVFKDGGFTSNDRSVRRYAIRKVLRQMDLGAELGAKTLVLWGGREGAEYDSAKDVSAALDRYREALNLLAQYSEDRGYGLRFAIEPKPNEPRGDILLPTAGHAIAFVQELERPELFGINPETGHEQMSNLNFTQGIAQALWHKKLFHIDLNGQHGPKFAQDLVFGHGDLLNAFSLVDLLENGPDGAPAYDGPRHFDYKPSRTEDYDGVWESAKANIRMYLLLKERAKAFRADPEVQEALAASKVAELKTPTLNPGEGYAELLADRSAFEDYDADAVGAKGFGFVKLNQLAIEHLLGAR 394
                                    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       392
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5XIN)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  XYLA_ACTM4 | P12851
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 Related Entries

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

UniProtKB/Swiss-Prot
        XYLA_ACTM4 | P12851: 1bhw 1xim 1xin 2xim 2xin 3xim 3xin 4xim 5xim 6xim 7xim 8xim 9xim

(-) Related Entries Specified in the PDB File

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