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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 :  03 Apr 92  (Deposition) - 15 Jul 93  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
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, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1MN8Ligand/IonMANGANESE (II) ION
2XLS4Ligand/IonD-XYLOSE (LINEAR FORM)

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP 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:255 , ASP A:292 , MN A:395 , MN A:396 , HOH A:454 , HOH A:455 , HOH A:530 , PHE B:26BINDING SITE FOR RESIDUE XLS A 397
02AC2SOFTWARETRP 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 , MN B:395 , MN B:396 , HOH B:457 , HOH B:458 , HOH B:534 , HOH B:561BINDING SITE FOR RESIDUE XLS B 397
03AC3SOFTWARETRP C:16 , HIS C:54 , TRP C:137 , GLU C:181 , LYS C:183 , GLU C:217 , HIS C:220 , ASP C:245 , ASP C:292 , MN C:395 , MN C:396 , HOH C:471 , HOH C:472 , HOH C:538 , HOH C:574 , PHE D:26BINDING SITE FOR RESIDUE XLS C 397
04AC4SOFTWAREPHE C:26 , TRP 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:255 , ASP D:292 , MN D:395 , MN D:396 , HOH D:482 , HOH D:483 , HOH D:549 , HOH D:586BINDING SITE FOR RESIDUE XLS D 397
05AC5SOFTWAREGLU A:181 , GLU A:217 , ASP A:245 , ASP A:292 , XLS A:397BINDING SITE FOR RESIDUE MN A 395
06AC6SOFTWAREGLU A:217 , HIS A:220 , ASP A:255 , ASP A:257 , XLS A:397 , HOH A:530BINDING SITE FOR RESIDUE MN A 396
07AC7SOFTWAREGLU B:181 , GLU B:217 , ASP B:245 , ASP B:292 , XLS B:397BINDING SITE FOR RESIDUE MN B 395
08AC8SOFTWAREGLU B:217 , HIS B:220 , ASP B:255 , ASP B:257 , XLS B:397 , HOH B:534BINDING SITE FOR RESIDUE MN B 396
09AC9SOFTWAREGLU C:181 , GLU C:217 , ASP C:245 , ASP C:292 , XLS C:397BINDING SITE FOR RESIDUE MN C 395
10BC1SOFTWAREGLU C:217 , HIS C:220 , ASP C:255 , ASP C:257 , XLS C:397 , HOH C:538BINDING SITE FOR RESIDUE MN C 396
11BC2SOFTWAREGLU D:181 , GLU D:217 , ASP D:245 , ASP D:292 , XLS D:397BINDING SITE FOR RESIDUE MN D 395
12BC3SOFTWAREGLU D:217 , HIS D:220 , ASP D:255 , ASP D:257 , XLS D:397 , HOH D:549BINDING SITE FOR RESIDUE MN D 396

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 9XIM)

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 9XIM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 9XIM)

(-) Exons   (0, 0)

(no "Exon" information available for 9XIM)

(-) 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 d9xima_ A: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 9ximA00 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.......hhhhhhhhhhhhhhhhhhhhhh...eeeee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........ee...hhhhhhhhhh...hhh.eee..hhhhhhh...hhhhhhhhhhhhh.....ee.................hhhhhhhhhhhhhh...........eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 9xim A   3 VQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIGAYGITFHDDDLVPFGSDAQTRDGIIAGFKKALDETGLIVPMVTTNLFTHPVFKDGGFTSNDRSVRRYAIRKVLRQMDLGAELGAKTLVLWGGREGAEYDSAKDVSAALDRYREALNLLAQYSEDRGYGLRFAIEPKPNQPRGDILLPTAGHAIAFVQELERPELFGINPETGHEQMSNLNFTQGIAQALWHKKLFHIDLNGQHGPKFDQDLVFGHGDLLNAFSLVDLLENGPDGAPAYDGPRHFDYKPSRTEDYDGVWESAKANIRMYLLLKERAKAFRADPEVQEALAASKVAELKTPTLNPGEGYAELLADRSAFEDYDADAVGAKGFGFVKLNQLAIEHLLGAR 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 d9ximb_ B: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 9ximB00 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.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........ee...hhhhhhhhhh...hhh.eee..hhhhhhh...hhhhhhhhhhhhh.....ee.................hhhhhhhhhhhhhh...........eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 9xim B   3 VQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIGAYGITFHDDDLVPFGSDAQTRDGIIAGFKKALDETGLIVPMVTTNLFTHPVFKDGGFTSNDRSVRRYAIRKVLRQMDLGAELGAKTLVLWGGREGAEYDSAKDVSAALDRYREALNLLAQYSEDRGYGLRFAIEPKPNQPRGDILLPTAGHAIAFVQELERPELFGINPETGHEQMSNLNFTQGIAQALWHKKLFHIDLNGQHGPKFDQDLVFGHGDLLNAFSLVDLLENGPDGAPAYDGPRHFDYKPSRTEDYDGVWESAKANIRMYLLLKERAKAFRADPEVQEALAASKVAELKTPTLNPGEGYAELLADRSAFEDYDADAVGAKGFGFVKLNQLAIEHLLGAR 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:391
                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d9ximc_ C: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 9ximC00 C:4-394 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...hhhhhhhh..hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 9xim C   4 QATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIGAYGITFHDDDLVPFGSDAQTRDGIIAGFKKALDETGLIVPMVTTNLFTHPVFKDGGFTSNDRSVRRYAIRKVLRQMDLGAELGAKTLVLWGGREGAEYDSAKDVSAALDRYREALNLLAQYSEDRGYGLRFAIEPKPNQPRGDILLPTAGHAIAFVQELERPELFGINPETGHEQMSNLNFTQGIAQALWHKKLFHIDLNGQHGPKFDQDLVFGHGDLLNAFSLVDLLENGPDGAPAYDGPRHFDYKPSRTEDYDGVWESAKANIRMYLLLKERAKAFRADPEVQEALAASKVAELKTPTLNPGEGYAELLADRSAFEDYDADAVGAKGFGFVKLNQLAIEHLLGAR 394
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393 


Chain D from PDB  Type:PROTEIN  Length:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d9ximd_ D: D-xylose isomerase                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 9ximD00 D:3-394 Divalent-metal-dependent TIM barrel enzymes                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eeeehhhhh...............hhhhhhhhhhhh...eee.hhhhhh....hhhhhhhhhhhhhhhhhhhh....eee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..eeeee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee...hhhhhhhhhh...hhh.eee..hhhhhhh...hhhhhhhhhhhhh.....ee.................hhhhhhhhhhhhhh...........eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 9xim D   3 VQATREDKFSFGLWTVGWQARDAFGDATRTALDPVEAVHKLAEIGAYGITFHDDDLVPFGSDAQTRDGIIAGFKKALDETGLIVPMVTTNLFTHPVFKDGGFTSNDRSVRRYAIRKVLRQMDLGAELGAKTLVLWGGREGAEYDSAKDVSAALDRYREALNLLAQYSEDRGYGLRFAIEPKPNQPRGDILLPTAGHAIAFVQELERPELFGINPETGHEQMSNLNFTQGIAQALWHKKLFHIDLNGQHGPKFDQDLVFGHGDLLNAFSLVDLLENGPDGAPAYDGPRHFDYKPSRTEDYDGVWESAKANIRMYLLLKERAKAFRADPEVQEALAASKVAELKTPTLNPGEGYAELLADRSAFEDYDADAVGAKGFGFVKLNQLAIEHLLGAR 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)
  - → 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, 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 9XIM)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  9xim
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  XYLA_ACTM4 | P12851
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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_ACTM4 | P12851: 1bhw 1xim 1xin 2xim 2xin 3xim 3xin 4xim 5xim 5xin 6xim 7xim 8xim

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 9XIM)