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(-) Description

Title :  1.9A CRYSTAL STRUCTURE OF UDP-GLUCOSE 4-EPIMERASE FROM BURKHOLDERIA PSEUDOMALLEI
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  25 Sep 08  (Deposition) - 28 Oct 08  (Release) - 08 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Burkholderia, Pseudomallei, Udp-Glucose, Epimerase, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Isomerase, Nad (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
1. 9A Crystal Structure Of Udp-Glucose 4-Epimerase From Burkholderia Pseudomallei
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UDP-GLUCOSE 4-EPIMERASE
    Chains: A, B
    EC Number: 5.1.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BURPS1710B_2458, BURPS1710B_3147, GALE, MSRB
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI 1710B
    Organism Taxid: 320372
    Strain: 1710B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2UPG2Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:11 , GLY A:14 , TYR A:15 , ILE A:16 , ASP A:35 , ASN A:36 , LEU A:37 , VAL A:38 , ASN A:39 , SER A:40 , THR A:61 , ASP A:62 , VAL A:63 , PHE A:84 , ALA A:85 , ALA A:86 , LYS A:88 , ASN A:103 , SER A:126 , SER A:127 , TYR A:152 , LYS A:156 , TYR A:180 , PHE A:181 , PRO A:183 , UPG A:342 , HOH A:343 , HOH A:346 , HOH A:365 , HOH A:411 , HOH A:420 , HOH A:497BINDING SITE FOR RESIDUE NAD A 341
2AC2SOFTWAREVAL A:90 , SER A:128 , THR A:130 , TYR A:152 , ASN A:182 , ASN A:201 , ASN A:202 , LEU A:203 , ARG A:219 , VAL A:220 , PHE A:221 , GLY A:232 , ARG A:234 , TYR A:236 , VAL A:272 , ARG A:295 , ASP A:298 , NAD A:341 , HOH A:362 , HOH A:388 , HOH A:397 , HOH A:427 , HOH A:495 , HOH A:514 , HOH A:533BINDING SITE FOR RESIDUE UPG A 342
3AC3SOFTWAREGLY B:11 , GLY B:14 , TYR B:15 , ILE B:16 , ASP B:35 , ASN B:36 , LEU B:37 , VAL B:38 , ASN B:39 , SER B:40 , THR B:61 , ASP B:62 , VAL B:63 , PHE B:84 , ALA B:85 , ALA B:86 , LYS B:88 , ASN B:103 , SER B:126 , SER B:127 , SER B:128 , TYR B:152 , LYS B:156 , TYR B:180 , PHE B:181 , PRO B:183 , UPG B:342 , HOH B:453 , HOH B:454 , HOH B:460 , HOH B:503 , HOH B:559 , HOH B:561BINDING SITE FOR RESIDUE NAD B 341
4AC4SOFTWARESER B:128 , THR B:130 , ASN B:182 , ASN B:201 , ASN B:202 , LEU B:203 , ARG B:219 , VAL B:220 , PHE B:221 , GLY B:232 , ARG B:234 , TYR B:236 , VAL B:272 , ARG B:295 , ASP B:298 , NAD B:341 , HOH B:500 , HOH B:504 , HOH B:575 , HOH B:585 , HOH B:590 , HOH B:602BINDING SITE FOR RESIDUE UPG B 342

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ENK)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:138 -Pro A:139
2Ser B:138 -Pro B:139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ENK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ENK)

(-) Exons   (0, 0)

(no "Exon" information available for 3ENK)

(-) 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:340
 aligned with Q3JPI3_BURP1 | Q3JPI3 from UniProtKB/TrEMBL  Length:340

    Alignment length:340
                                    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
         Q3JPI3_BURP1     1 MSTKGTILVTGGAGYIGSHTAVELLAHGYDVVIADNLVNSKREAIARIEKITGKTPAFHETDVSDERALARIFDAHPITAAIHFAALKAVGESVAKPIEYYRNNLDSLLSLLRVMRERAVKRIVFSSSATVYGVPERSPIDETFPLSATNPYGQTKLMAEQILRDVEAADPSWRVATLRYFNPVGAHESGLIGEDPAGIPNNLMPYVAQVAVGKLEKLRVFGSDYPTPDGTGVRDYIHVVDLARGHIAALDALERRDASLTVNLGTGRGYSVLEVVRAFEKASGRAVPYELVARRPGDVAECYANPAAAAETIGWKAERDLERMCADHWRWQENNPRGFV 340
               SCOP domains d3enka_ A: automated matches                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ----3enkA01 A:5-184,A:235-265 NAD(P)-binding Rossmann-like Domain                                                                                                                       3enkA02 A:185-234,A:266-340                       3enkA01 A:5-184,A:235-265      3enkA02 A:185-234,A:266-340 UDP-galactose 4-epimerase, domain 1             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhh...eee.....hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhh...eeeeeee.eee.................hhhhhhhhhhh.....eeee...........ee.eeehhhhhhhhhhhhhhhhhhh..eeeee.....eehhhhhhhhhhhhh....eeee........ee...hhhhhhhhh.....hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3enk A   1 MSTKGTILVTGGAGYIGSHTAVELLAHGYDVVIADNLVNSKREAIARIEKITGKTPAFHETDVSDERALARIFDAHPITAAIHFAALKAVGESVAKPIEYYRNNLDSLLSLLRVMRERAVKRIVFSSSATVYGVPERSPIDETFPLSATNPYGQTKLMAEQILRDVEAADPSWRVATLRYFNPVGAHESGLIGEDPAGIPNNLMPYVAQVAVGKLEKLRVFGSDYPTPDGTGVRDYIHVVDLARGHIAALDALERRDASLTVNLGTGRGYSVLEVVRAFEKASGRAVPYELVARRPGDVAECYANPAAAAETIGWKAERDLERMCADHWRWQENNPRGFV 340
                                    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


Chain B from PDB  Type:PROTEIN  Length:339
 aligned with Q3JPI3_BURP1 | Q3JPI3 from UniProtKB/TrEMBL  Length:340

    Alignment length:339
                                    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         
         Q3JPI3_BURP1     1 MSTKGTILVTGGAGYIGSHTAVELLAHGYDVVIADNLVNSKREAIARIEKITGKTPAFHETDVSDERALARIFDAHPITAAIHFAALKAVGESVAKPIEYYRNNLDSLLSLLRVMRERAVKRIVFSSSATVYGVPERSPIDETFPLSATNPYGQTKLMAEQILRDVEAADPSWRVATLRYFNPVGAHESGLIGEDPAGIPNNLMPYVAQVAVGKLEKLRVFGSDYPTPDGTGVRDYIHVVDLARGHIAALDALERRDASLTVNLGTGRGYSVLEVVRAFEKASGRAVPYELVARRPGDVAECYANPAAAAETIGWKAERDLERMCADHWRWQENNPRGF 339
               SCOP domains d3enkb_ B: automated matches                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----3enkB01 B:5-184,B:235-265 NAD(P)-binding Rossmann-like Domain                                                                                                                       3enkB02 B:185-234,B:266-339                       3enkB01 B:5-184,B:235-265      3enkB02 B:185-234,B:266-339 UDP-galactose 4-epimerase, domain 1            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhh...eee.....hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhh...eeeeeee.eee.................hhhhhhhhhhhh....eeee...........ee.eeehhhhhhhhhhhhhhhhhh...eeeee.....eehhhhhhhhhhhhh....eeee........ee...hhhhhhhhh.....hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3enk B   1 MSTKGTILVTGGAGYIGSHTAVELLAHGYDVVIADNLVNSKREAIARIEKITGKTPAFHETDVSDERALARIFDAHPITAAIHFAALKAVGESVAKPIEYYRNNLDSLLSLLRVMRERAVKRIVFSSSATVYGVPERSPIDETFPLSATNPYGQTKLMAEQILRDVEAADPSWRVATLRYFNPVGAHESGLIGEDPAGIPNNLMPYVAQVAVGKLEKLRVFGSDYPTPDGTGVRDYIHVVDLARGHIAALDALERRDASLTVNLGTGRGYSVLEVVRAFEKASGRAVPYELVARRPGDVAECYANPAAAAETIGWKAERDLERMCADHWRWQENNPRGF 339
                                    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
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ENK)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q3JPI3_BURP1 | Q3JPI3)
molecular function
    GO:0003978    UDP-glucose 4-epimerase activity    Catalysis of the reaction: UDP-glucose = UDP-galactose.
    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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0006012    galactose metabolic process    The chemical reactions and pathways involving galactose, the aldohexose galacto-hexose. D-galactose is widely distributed in combined form in plants, animals and microorganisms as a constituent of oligo- and polysaccharides; it also occurs in galactolipids and as its glucoside in lactose and melibiose.

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