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(-) Description

Title :  STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH NAD+
 
Authors :  J. B. Thoden, T. M. Wohlers, J. L. Fridovich-Keil, H. M. Holden
Date :  06 Mar 00  (Deposition) - 17 May 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Short-Chain Dehydrogenase, Epimerase, Galactosemia, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. B. Thoden, T. M. Wohlers, J. L. Fridovich-Keil, H. M. Holden
Crystallographic Evidence For Tyr 157 Functioning As The Active Site Base In Human Udp-Galactose 4-Epimerase.
Biochemistry V. 39 5691 2000
PubMed-ID: 10801319  |  Reference-DOI: 10.1021/BI000215L
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UDP-GALACTOSE 4-EPIMERASE
    ChainsA
    EC Number5.1.3.2
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System Taxid4932
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    TissueFORESKIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:9 , GLY A:12 , TYR A:13 , ILE A:14 , ASP A:33 , ASN A:34 , PHE A:35 , HIS A:36 , ASN A:37 , ALA A:38 , MET A:65 , ASP A:66 , ILE A:67 , PHE A:88 , GLY A:90 , LYS A:92 , SER A:130 , SER A:131 , TYR A:157 , LYS A:161 , TYR A:185 , PHE A:186 , PRO A:188 , ASN A:206 , HOH A:605 , HOH A:606 , HOH A:625 , HOH A:631 , HOH A:653 , HOH A:655 , HOH A:656 , HOH A:658 , HOH A:660BINDING SITE FOR RESIDUE NAD A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EK5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:142 -Pro A:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (17, 17)

Asymmetric Unit (17, 17)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_037733A25VGALE_HUMANDisease (EDG)  ---AA25V
02UniProtVAR_002539N34SGALE_HUMANDisease (EDG)121908046AN34S
03UniProtVAR_037734R40CGALE_HUMANDisease (EDG)144492228AR40C
04UniProtVAR_037735D69EGALE_HUMANDisease (EDG)  ---AD69E
05UniProtVAR_002540G90EGALE_HUMANDisease (EDG)28940882AG90E
06UniProtVAR_010058V94MGALE_HUMANDisease (EDG)121908047AV94M
07UniProtVAR_002541D103GGALE_HUMANDisease (EDG)28940883AD103G
08UniProtVAR_037736E165KGALE_HUMANDisease (EDG)528467258AE165K
09UniProtVAR_037737R169WGALE_HUMANDisease (EDG)137853859AR169W
10UniProtVAR_002542A180VGALE_HUMANPolymorphism3204468AA180V
11UniProtVAR_002543L183PGALE_HUMANDisease (EDG)121908045AL183P
12UniProtVAR_037738R239WGALE_HUMANDisease (EDG)137853860AR239W
13UniProtVAR_002544K257RGALE_HUMANDisease (EDG)28940884AK257R
14UniProtVAR_037739G302DGALE_HUMANDisease (EDG)137853861AG302D
15UniProtVAR_002545L313MGALE_HUMANDisease (EDG)3180383AL313M
16UniProtVAR_002546G319EGALE_HUMANDisease (EDG)28940885AG319E
17UniProtVAR_037740R335HGALE_HUMANDisease (EDG)368637540AR335H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (17, 34)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_037733A25VGALE_HUMANDisease (EDG)  ---AA25V
02UniProtVAR_002539N34SGALE_HUMANDisease (EDG)121908046AN34S
03UniProtVAR_037734R40CGALE_HUMANDisease (EDG)144492228AR40C
04UniProtVAR_037735D69EGALE_HUMANDisease (EDG)  ---AD69E
05UniProtVAR_002540G90EGALE_HUMANDisease (EDG)28940882AG90E
06UniProtVAR_010058V94MGALE_HUMANDisease (EDG)121908047AV94M
07UniProtVAR_002541D103GGALE_HUMANDisease (EDG)28940883AD103G
08UniProtVAR_037736E165KGALE_HUMANDisease (EDG)528467258AE165K
09UniProtVAR_037737R169WGALE_HUMANDisease (EDG)137853859AR169W
10UniProtVAR_002542A180VGALE_HUMANPolymorphism3204468AA180V
11UniProtVAR_002543L183PGALE_HUMANDisease (EDG)121908045AL183P
12UniProtVAR_037738R239WGALE_HUMANDisease (EDG)137853860AR239W
13UniProtVAR_002544K257RGALE_HUMANDisease (EDG)28940884AK257R
14UniProtVAR_037739G302DGALE_HUMANDisease (EDG)137853861AG302D
15UniProtVAR_002545L313MGALE_HUMANDisease (EDG)3180383AL313M
16UniProtVAR_002546G319EGALE_HUMANDisease (EDG)28940885AG319E
17UniProtVAR_037740R335HGALE_HUMANDisease (EDG)368637540AR335H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EK5)

(-) Exons   (10, 10)

Asymmetric Unit (10, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1jENST000003744971jENSE00001850298chr1:24126892-2412687716GALE_HUMAN-00--
1.1nENST000003744971nENSE00001372948chr1:24125926-2412585671GALE_HUMAN-00--
1.2bENST000003744972bENSE00002180266chr1:24125502-24125377126GALE_HUMAN1-41411A:1-4141
1.2eENST000003744972eENSE00001691927chr1:24125220-24125105116GALE_HUMAN41-79391A:41-7939
1.2hENST000003744972hENSE00000758318chr1:24124720-24124607114GALE_HUMAN80-117381A:80-11738
1.3bENST000003744973bENSE00000758319chr1:24124361-24124185177GALE_HUMAN118-176591A:118-17659
1.4dENST000003744974dENSE00000758320chr1:24123637-24123524114GALE_HUMAN177-214381A:177-21438
1.5ENST000003744975ENSE00000758321chr1:24123432-2412336667GALE_HUMAN215-237231A:215-23723
1.6aENST000003744976aENSE00000758322chr1:24123272-2412318786GALE_HUMAN237-265291A:237-26529
1.6dENST000003744976dENSE00002163869chr1:24123076-2412299978GALE_HUMAN266-291261A:266-29126
1.6eENST000003744976eENSE00002170745chr1:24122755-24122641115GALE_HUMAN292-330391A:292-33039
1.6hENST000003744976hENSE00001893164chr1:24122497-24122090408GALE_HUMAN330-348191A:330-34617

(-) 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:346
 aligned with GALE_HUMAN | Q14376 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:346
                                    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      
           GALE_HUMAN     1 MAEKVLVTGGAGYIGSHTVLELLEAGYLPVVIDNFHNAFRGGGSLPESLRRVQELTGRSVEFEEMDILDQGALQRLFKKYSFMAVIHFAGLKAVGESVQKPLDYYRVNLTGTIQLLEIMKAHGVKNLVFSSSATVYGNPQYLPLDEAHPTGGCTNPYGKSKFFIEEMIRDLCQADKTWNAVLLRYFNPTGAHASGCIGEDPQGIPNNLMPYVSQVAIGRREALNVFGNDYDTEDGTGVRDYIHVVDLAKGHIAALRKLKEQCGCRIYNLGTGTGYSVLQMVQAMEKASGKKIPYKVVARREGDVAACYANPSLAQEELGWTAALGLDRMCEDLWRWQKQNPSGFGT 346
               SCOP domains d1ek5a_ A: Uridine diphosphogalactose-4-epimerase (UDP-galactose 4-epimerase)                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --1ek5A02 A:3-189,A:240-270 NAD(P)-binding Rossmann-like Domain                                                                                                                              1ek5A01 A:190-239,A:271-346                       1ek5A02 A:3-189,A:240-270      1ek5A01 A:190-239,A:271-346 UDP-galactose 4-epimerase, domain 1              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee............hhhhhhhhhhhh...eeee....hhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhh.................hhhhhhhhhhhhhhhhhhhhh...eeeeee..eee..................hhhhhhhhhh.....eeee...........ee.eeehhhhhhhhhhhhhhhhh...eeeee......eehhhhhhhhhhhhh....eeee........ee...hhhhhhhhh.....hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------V--------S-----C----------------------------E--------------------E---M--------G-------------------------------------------------------------K---W----------V--P-------------------------------------------------------W-----------------R--------------------------------------------D----------M-----E---------------H----------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:1-41 UniProt: 1-41     --------------------------------------Exon 1.2h  PDB: A:80-117              Exon 1.3b  PDB: A:118-176 UniProt: 118-176                 Exon 1.4d  PDB: A:177-214             Exon 1.5  PDB: A:215-23----------------------------Exon 1.6d  PDB: A:266-291 Exon 1.6e  PDB: A:292-330              ---------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.2e  PDB: A:41-79 UniProt: 41-79 -------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6a  PDB: A:237-265    ----------------------------------------------------------------Exon 1.6h         Transcript 1 (2)
                 1ek5 A   1 MAEKVLVTGGAGYIGSHTVLELLEAGYLPVVIDNFHNAFRGGGSLPESLRRVQELTGRSVEFEEMDILDQGALQRLFKKYSFMAVIHFAGLKAVGESVQKPLDYYRVNLTGTIQLLEIMKAHGVKNLVFSSSATVYGNPQYLPLDEAHPTGGCTNPYGKSKFFIEEMIRDLCQADKTWNAVLLRYFNPTGAHASGCIGEDPQGIPNNLMPYVSQVAIGRREALNVFGNDYDTEDGTGVRDYIHVVDLAKGHIAALRKLKEQCGCRIYNLGTGTGYSVLQMVQAMEKASGKKIPYKVVARREGDVAACYANPSLAQEELGWTAALGLDRMCEDLWRWQKQNPSGFGT 346
                                    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      

   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, 1)

Asymmetric Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EK5)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (GALE_HUMAN | Q14376)
molecular function
    GO:0003974    UDP-N-acetylglucosamine 4-epimerase activity    Catalysis of the reaction: UDP-N-acetyl-D-glucosamine = UDP-N-acetyl-D-galactosamine.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0016857    racemase and epimerase activity, acting on carbohydrates and derivatives    Catalysis of a reaction that alters the configuration of one or more chiral centers in a carbohydrate molecule.
biological process
    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:0019388    galactose catabolic process    The chemical reactions and pathways resulting in the breakdown of galactose, the aldohexose galacto-hexose.
    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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GALE_HUMAN | Q143761ek6 1hzj 1i3k 1i3l 1i3m 1i3n

(-) Related Entries Specified in the PDB File

1ek6