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(-) Description

Title :  HUMAN UDP-GALACTOSE 4-EPIMERASE: ACCOMMODATION OF UDP-N-ACETYLGLUCOSAMINE WITHIN THE ACTIVE SITE
 
Authors :  J. B. Thoden, T. M. Wohlers, J. L. Fridovich-Keil, H. M. Holden
Date :  25 Jan 01  (Deposition) - 09 May 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Epimerase, Short-Chain Dehydrogenase, Galactosemia, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. B. Thoden, T. M. Wohlers, J. L. Fridovich-Keil, H. M. Holden
Human Udp-Galactose 4-Epimerase. Accommodation Of Udp-N-Acetylglucosamine Within The Active Site.
J. Biol. Chem. V. 276 15131 2001
PubMed-ID: 11279032  |  Reference-DOI: 10.1074/JBC.M100220200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UDP-GALACTOSE 4-EPIMERASE
    ChainsA, B
    EC Number5.1.3.2
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPIC3.5KHGALE
    Expression System StrainGS115
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUDP-GLUCOSE 4-EPIMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2MG1Ligand/IonMAGNESIUM ION
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4UD12Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:100 , PRO A:101 , LEU A:102 , HOH B:1278BINDING SITE FOR RESIDUE CL A 950
2AC2SOFTWAREHOH A:1349 , LYS B:100 , PRO B:101 , LEU B:102BINDING SITE FOR RESIDUE CL B 951
3AC3SOFTWARELYS A:4 , TYR A:80 , SER A:81BINDING SITE FOR RESIDUE CL A 952
4AC4SOFTWAREHOH A:1287 , HOH A:1292 , HOH A:1313 , HOH A:1409 , HOH A:1749 , HOH A:1941BINDING SITE FOR RESIDUE MG A 960
5AC5SOFTWAREGLY 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 , MET A:65 , ASP A:66 , ILE A:67 , PHE A:88 , ALA A:89 , GLY A:90 , LYS A:92 , SER A:130 , SER A:131 , SER A:132 , TYR A:157 , LYS A:161 , TYR A:185 , PRO A:188 , UD1 A:401 , HOH A:1101 , HOH A:1104 , HOH A:1113 , HOH A:1129 , HOH A:1141 , HOH A:1161 , HOH A:1203 , HOH A:1335 , HOH A:1482 , HOH A:1518BINDING SITE FOR RESIDUE NAD A 400
6AC6SOFTWAREVAL A:94 , SER A:132 , THR A:134 , ASN A:187 , ASN A:206 , ASN A:207 , LEU A:208 , LEU A:223 , ASN A:224 , VAL A:225 , PHE A:226 , GLY A:237 , ARG A:239 , TYR A:241 , VAL A:277 , ARG A:300 , ASP A:303 , NAD A:400 , HOH A:1189 , HOH A:1206 , HOH A:1208 , HOH A:1254 , HOH A:1308 , HOH A:1518 , HOH A:1519 , HOH A:1534 , HOH A:1598 , HOH A:1775BINDING SITE FOR RESIDUE UD1 A 401
7AC7SOFTWAREGLY B:9 , GLY B:12 , TYR B:13 , ILE B:14 , ASP B:33 , ASN B:34 , HIS B:36 , ASN B:37 , MET B:65 , ASP B:66 , ILE B:67 , PHE B:88 , ALA B:89 , GLY B:90 , LYS B:92 , SER B:130 , SER B:131 , TYR B:157 , LYS B:161 , TYR B:185 , PHE B:186 , PRO B:188 , UD1 B:901 , HOH B:1100 , HOH B:1105 , HOH B:1122 , HOH B:1194 , HOH B:1299 , HOH B:1643BINDING SITE FOR RESIDUE NAD B 900
8AC8SOFTWARELYS B:92 , VAL B:94 , SER B:132 , TYR B:157 , TYR B:185 , PHE B:186 , ASN B:187 , ASN B:206 , ASN B:207 , LEU B:208 , ASN B:224 , VAL B:225 , PHE B:226 , GLY B:237 , ARG B:239 , TYR B:241 , ARG B:300 , ASP B:303 , NAD B:900 , HOH B:1121 , HOH B:1135 , HOH B:1158 , HOH B:1200 , HOH B:1204 , HOH B:1228 , HOH B:1255 , HOH B:1698BINDING SITE FOR RESIDUE UD1 B 901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:142 -Pro A:143
2Leu B:142 -Pro B:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (17, 34)

Asymmetric/Biological Unit (17, 34)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_037733A25VGALE_HUMANDisease (EDG)  ---A/BA25V
02UniProtVAR_002539N34SGALE_HUMANDisease (EDG)121908046A/BN34S
03UniProtVAR_037734R40CGALE_HUMANDisease (EDG)144492228A/BR40C
04UniProtVAR_037735D69EGALE_HUMANDisease (EDG)  ---A/BD69E
05UniProtVAR_002540G90EGALE_HUMANDisease (EDG)28940882A/BG90E
06UniProtVAR_010058V94MGALE_HUMANDisease (EDG)121908047A/BV94M
07UniProtVAR_002541D103GGALE_HUMANDisease (EDG)28940883A/BD103G
08UniProtVAR_037736E165KGALE_HUMANDisease (EDG)528467258A/BE165K
09UniProtVAR_037737R169WGALE_HUMANDisease (EDG)137853859A/BR169W
10UniProtVAR_002542A180VGALE_HUMANPolymorphism3204468A/BV180V
11UniProtVAR_002543L183PGALE_HUMANDisease (EDG)121908045A/BL183P
12UniProtVAR_037738R239WGALE_HUMANDisease (EDG)137853860A/BR239W
13UniProtVAR_002544K257RGALE_HUMANDisease (EDG)28940884A/BK257R
14UniProtVAR_037739G302DGALE_HUMANDisease (EDG)137853861A/BG302D
15UniProtVAR_002545L313MGALE_HUMANDisease (EDG)3180383A/BL313M
16UniProtVAR_002546G319EGALE_HUMANDisease (EDG)28940885A/BG319E
17UniProtVAR_037740R335HGALE_HUMANDisease (EDG)368637540A/BR335H

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (10, 20)

Asymmetric/Biological Unit (10, 20)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1jENST000003744971jENSE00001850298chr1:24126892-2412687716GALE_HUMAN-00--
1.1nENST000003744971nENSE00001372948chr1:24125926-2412585671GALE_HUMAN-00--
1.2bENST000003744972bENSE00002180266chr1:24125502-24125377126GALE_HUMAN1-41412A:2-41
B:2-41
40
40
1.2eENST000003744972eENSE00001691927chr1:24125220-24125105116GALE_HUMAN41-79392A:41-79
B:41-79
39
39
1.2hENST000003744972hENSE00000758318chr1:24124720-24124607114GALE_HUMAN80-117382A:80-117
B:80-117
38
38
1.3bENST000003744973bENSE00000758319chr1:24124361-24124185177GALE_HUMAN118-176592A:118-176
B:118-176
59
59
1.4dENST000003744974dENSE00000758320chr1:24123637-24123524114GALE_HUMAN177-214382A:177-214
B:177-214
38
38
1.5ENST000003744975ENSE00000758321chr1:24123432-2412336667GALE_HUMAN215-237232A:215-237
B:215-237
23
23
1.6aENST000003744976aENSE00000758322chr1:24123272-2412318786GALE_HUMAN237-265292A:237-265
B:237-265
29
29
1.6dENST000003744976dENSE00002163869chr1:24123076-2412299978GALE_HUMAN266-291262A:266-291
B:266-291
26
26
1.6eENST000003744976eENSE00002170745chr1:24122755-24122641115GALE_HUMAN292-330392A:292-330
B:292-330
39
39
1.6hENST000003744976hENSE00001893164chr1:24122497-24122090408GALE_HUMAN330-348192A:330-346
B:330-346
17
17

(-) 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:345
 aligned with GALE_HUMAN | Q14376 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:345
                                    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     
           GALE_HUMAN     2 AEKVLVTGGAGYIGSHTVLELLEAGYLPVVIDNFHNAFRGGGSLPESLRRVQELTGRSVEFEEMDILDQGALQRLFKKYSFMAVIHFAGLKAVGESVQKPLDYYRVNLTGTIQLLEIMKAHGVKNLVFSSSATVYGNPQYLPLDEAHPTGGCTNPYGKSKFFIEEMIRDLCQADKTWNAVLLRYFNPTGAHASGCIGEDPQGIPNNLMPYVSQVAIGRREALNVFGNDYDTEDGTGVRDYIHVVDLAKGHIAALRKLKEQCGCRIYNLGTGTGYSVLQMVQAMEKASGKKIPYKVVARREGDVAACYANPSLAQEELGWTAALGLDRMCEDLWRWQKQNPSGFGT 346
               SCOP domains d1hzja_ A: Uridine diphosphogalactose-4-epimerase (UDP-galactose 4-epimerase)                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -1hzjA02 A:3-189,A:240-270 NAD(P)-binding Rossmann-like Domain                                                                                                                              1hzjA01 A:190-239,A:271-346                       1hzjA02 A:3-189,A:240-270      1hzjA01 A:190-239,A:271-346 UDP-galactose 4-epimerase, domain 1              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhh...eeee....hhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhh.................hhhhhhhhhhhhhhhhhhhhh...eeeeeee.eee.................hhhhhhhhhhh.....eeee...........ee.eeehhhhhhhhhhhhhhhhh...eeeeee.....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:2-41 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)
                 1hzj A   2 AEKVLVTGGAGYIGSHTVLELLEAGYLPVVIDNFHNAFRGGGSLPESLRRVQELTGRSVEFEEMDILDQGALQRLFKKYSFMAVIHFAGLKAVGESVQKPLDYYRVNLTGTIQLLEIMKAHGVKNLVFSSSATVYGNPQYLPLDEAHPTGGCTNPYGKSKFFIEEMIRDLCQADKTWNVVLLRYFNPTGAHASGCIGEDPQGIPNNLMPYVSQVAIGRREALNVFGNDYDTEDGTGVRDYIHVVDLAKGHIAALRKLKEQCGCRIYNLGTGTGYSVLQMVQAMEKASGKKIPYKVVARREGDVAACYANPSLAQEELGWTAALGLDRMCEDLWRWQKQNPSGFGT 346
                                    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     

Chain B from PDB  Type:PROTEIN  Length:345
 aligned with GALE_HUMAN | Q14376 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:345
                                    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     
           GALE_HUMAN     2 AEKVLVTGGAGYIGSHTVLELLEAGYLPVVIDNFHNAFRGGGSLPESLRRVQELTGRSVEFEEMDILDQGALQRLFKKYSFMAVIHFAGLKAVGESVQKPLDYYRVNLTGTIQLLEIMKAHGVKNLVFSSSATVYGNPQYLPLDEAHPTGGCTNPYGKSKFFIEEMIRDLCQADKTWNAVLLRYFNPTGAHASGCIGEDPQGIPNNLMPYVSQVAIGRREALNVFGNDYDTEDGTGVRDYIHVVDLAKGHIAALRKLKEQCGCRIYNLGTGTGYSVLQMVQAMEKASGKKIPYKVVARREGDVAACYANPSLAQEELGWTAALGLDRMCEDLWRWQKQNPSGFGT 346
               SCOP domains d1hzjb_ B: Uridine diphosphogalactose-4-epimerase (UDP-galactose 4-epimerase)                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -1hzjB02 B:3-189,B:240-270 NAD(P)-binding Rossmann-like Domain                                                                                                                              1hzjB01 B:190-239,B:271-346                       1hzjB02 B:3-189,B:240-270      1hzjB01 B:190-239,B:271-346 UDP-galactose 4-epimerase, domain 1              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhh...eeee....hhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh.................hhhhhhhhhhhhhhhhhhhhh...eeeeeee.eee.................hhhhhhhhhhh.....eeee...........eeeeeehhhhhhhhhhhhhhhh....eeeeee....eeehhhhhhhhhhhhh....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: B:2-41 UniProt: 1-41    --------------------------------------Exon 1.2h  PDB: B:80-117              Exon 1.3b  PDB: B:118-176 UniProt: 118-176                 Exon 1.4d  PDB: B:177-214             Exon 1.5  PDB: B:215-23----------------------------Exon 1.6d  PDB: B:266-291 Exon 1.6e  PDB: B:292-330              ---------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.2e  PDB: B:41-79 UniProt: 41-79 -------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6a  PDB: B:237-265    ----------------------------------------------------------------Exon 1.6h         Transcript 1 (2)
                 1hzj B   2 AEKVLVTGGAGYIGSHTVLELLEAGYLPVVIDNFHNAFRGGGSLPESLRRVQELTGRSVEFEEMDILDQGALQRLFKKYSFMAVIHFAGLKAVGESVQKPLDYYRVNLTGTIQLLEIMKAHGVKNLVFSSSATVYGNPQYLPLDEAHPTGGCTNPYGKSKFFIEEMIRDLCQADKTWNVVLLRYFNPTGAHASGCIGEDPQGIPNNLMPYVSQVAIGRREALNVFGNDYDTEDGTGVRDYIHVVDLAKGHIAALRKLKEQCGCRIYNLGTGTGYSVLQMVQAMEKASGKKIPYKVVARREGDVAACYANPSLAQEELGWTAALGLDRMCEDLWRWQKQNPSGFGT 346
                                    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     

   Legend:   → Mismatch (orange background)
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    → 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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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 | Q143761ek5 1ek6 1i3k 1i3l 1i3m 1i3n

(-) Related Entries Specified in the PDB File

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