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(-) Description

Title :  UDP-GALACTOSE 4-EPIMERASE COMPLEXED WITH UDP-PHENOL
 
Authors :  J. B. Thoden, A. M. Gulick, H. M. Holden
Date :  08 Mar 97  (Deposition) - 18 Mar 98  (Release) - 27 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Udp-Galactose, Epimerase, Isomerase, Galactose Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Thoden, P. A. Frey, H. M. Holden
High-Resolution X-Ray Structure Of Udp-Galactose 4-Epimeras Complexed With Udp-Phenol.
Protein Sci. V. 5 2149 1996
PubMed-ID: 8931134

(-) Compounds

Molecule 1 - UDP-GALACTOSE 4-EPIMERASE
    Cell Line: BL21
    Chains: A, B
    EC Number: 5.1.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3) PLYSS CELLS
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: EPIMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2NA1Ligand/IonSODIUM ION
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4UPP2Ligand/IonPHENYL-URIDINE-5'-DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:91 , HOH A:440 , HOH A:441 , HOH A:616 , HOH A:694 , HOH B:413BINDING SITE FOR RESIDUE NA B 411
2AC2SOFTWAREGLY A:7 , GLY A:10 , TYR A:11 , ILE A:12 , ASP A:31 , ASN A:32 , LEU A:33 , CYS A:34 , ASN A:35 , SER A:36 , GLY A:57 , ASP A:58 , ILE A:59 , PHE A:80 , ALA A:81 , GLY A:82 , LYS A:84 , ASN A:99 , SER A:122 , SER A:123 , SER A:124 , TYR A:149 , LYS A:153 , TYR A:177 , PHE A:178 , UPP A:341 , HOH A:352 , HOH A:368 , HOH A:420 , HOH A:422BINDING SITE FOR RESIDUE NAD A 340
3AC3SOFTWARELYS A:84 , TYR A:149 , ASN A:179 , ASN A:198 , ASN A:199 , LEU A:200 , ALA A:216 , ILE A:217 , PHE A:218 , GLY A:229 , ARG A:231 , TYR A:233 , VAL A:269 , ARG A:292 , ASP A:295 , NAD A:340 , HOH A:427 , HOH A:429 , HOH A:492 , HOH A:494 , HOH A:511 , HOH A:550 , HOH A:551BINDING SITE FOR RESIDUE UPP A 341
4AC4SOFTWAREGLY B:7 , GLY B:10 , TYR B:11 , ILE B:12 , ASP B:31 , ASN B:32 , LEU B:33 , CYS B:34 , ASN B:35 , SER B:36 , GLY B:57 , ASP B:58 , ILE B:59 , PHE B:80 , ALA B:81 , GLY B:82 , LYS B:84 , ASN B:99 , SER B:122 , SER B:123 , SER B:124 , TYR B:149 , LYS B:153 , TYR B:177 , PHE B:178 , UPP B:341 , HOH B:435 , HOH B:436 , HOH B:494 , HOH B:496 , HOH B:521 , HOH B:609 , HOH B:726BINDING SITE FOR RESIDUE NAD B 340
5AC5SOFTWAREVAL B:86 , ASN B:179 , ASN B:198 , ASN B:199 , LEU B:200 , LEU B:215 , ALA B:216 , ILE B:217 , PHE B:218 , GLY B:229 , ARG B:231 , TYR B:233 , ARG B:292 , ASP B:295 , TYR B:299 , NAD B:340 , HOH B:497 , HOH B:553 , HOH B:583 , HOH B:595 , HOH B:663 , HOH B:672BINDING SITE FOR RESIDUE UPP B 341
6AC6SOFTWAREALA A:208 , THR B:315 , GLU B:320 , HOH B:678BINDING SITE FOR RESIDUE EDO B 410

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2UDP)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:134 -Pro A:135
2Ile B:134 -Pro B:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2UDP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2UDP)

(-) Exons   (0, 0)

(no "Exon" information available for 2UDP)

(-) 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:338
 aligned with GALE_ECOLI | P09147 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:338
                                    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        
           GALE_ECOLI     1 MRVLVTGGSGYIGSHTCVQLLQNGHDVIILDNLCNSKRSVLPVIERLGGKHPTFVEGDIRNEALMTEILHDHAIDTVIHFAGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNFIFSSSATVYGDQPKIPYVESFPTGTPQSPYGKSKLMVEQILTDLQKAQPDWSIALLRYFNPVGAHPSGDMGEDPQGIPNNLMPYIAQVAVGRRDSLAIFGNDYPTEDGTGVRDYIHVMDLADGHVVAMEKLANKPGVHIYNLGAGVGNSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYWADASKADRELNWRVTRTLDEMAQDTWHWQSRHPQGYPD 338
               SCOP domains d2udpa_ A: Uridine diphosphogalactose-4-epimerase (UDP-galactose 4-epimerase)                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2udpA02 A:1-181,A:232-262 NAD(P)-binding Rossmann-like Domain                                                                                                                        2udpA01 A:182-231,A:263-338                       2udpA02 A:1-181,A:232-262      2udpA01 A:182-231,A:263-338 UDP-galactose 4-epimerase, domain 1              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhh...eeeeee......hhhhhhhhhhh....eeee.....hhhhhhhhhh....eeee......hhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhh...................hhhhhhhhhhhhhhhhhhh....eeeeeee.eee..................hhhhhhhhh......eeee..............eeehhhhhhhhhhhhhhh....eeeeeee.......hhhhhhhhhhhh.....eeee..............hhhhhhh.......hhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2udp A   1 MRVLVTGGSGYIGSHTCVQLLQNGHDVIILDNLCNSKRSVLPVIERLGGKHPTFVEGDIRNEALMTEILHDHAIDTVIHFAGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNFIFSSSATVYGDQPKIPYVESFPTGTPQSPYGKSKLMVEQILTDLQKAQPDWSIALLRYFNPVGAHPSGDMGEDPQGIPNNLMPYIAQVAVGRRDSLAIFGNDYPTEDGTGVRDYIHVMDLADGHVVAMEKLANKPGVHIYNLGAGVGNSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYWADASKADRELNWRVTRTLDEMAQDTWHWQSRHPQGYPD 338
                                    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        


Chain B from PDB  Type:PROTEIN  Length:338
 aligned with GALE_ECOLI | P09147 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:338
                                    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        
           GALE_ECOLI     1 MRVLVTGGSGYIGSHTCVQLLQNGHDVIILDNLCNSKRSVLPVIERLGGKHPTFVEGDIRNEALMTEILHDHAIDTVIHFAGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNFIFSSSATVYGDQPKIPYVESFPTGTPQSPYGKSKLMVEQILTDLQKAQPDWSIALLRYFNPVGAHPSGDMGEDPQGIPNNLMPYIAQVAVGRRDSLAIFGNDYPTEDGTGVRDYIHVMDLADGHVVAMEKLANKPGVHIYNLGAGVGNSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYWADASKADRELNWRVTRTLDEMAQDTWHWQSRHPQGYPD 338
               SCOP domains d2udpb_ B: Uridine diphosphogalactose-4-epimerase (UDP-galactose 4-epimerase)                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2udpB02 B:1-181,B:232-262 NAD(P)-binding Rossmann-like Domain                                                                                                                        2udpB01 B:182-231,B:263-338                       2udpB02 B:1-181,B:232-262      2udpB01 B:182-231,B:263-338 UDP-galactose 4-epimerase, domain 1              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhh...eeeeee......hhhhhhhhhhh....eeee.....hhhhhhhhhh....eeee......hhhhhh.hhhhhhhhhhhhhhhhhhhhh....eeeeeeehhhh...................hhhhhhhhhhhhhhhhhhh....eeeeeee.eee..................hhhhhhhhh......eeee..............eeehhhhhhhhhhhhhhh....eeeeeee.......hhhhhhhhhhhh.....eeee..............hhhhhhh.......hhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2udp B   1 MRVLVTGGSGYIGSHTCVQLLQNGHDVIILDNLCNSKRSVLPVIERLGGKHPTFVEGDIRNEALMTEILHDHAIDTVIHFAGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNFIFSSSATVYGDQPKIPYVESFPTGTPQSPYGKSKLMVEQILTDLQKAQPDWSIALLRYFNPVGAHPSGDMGEDPQGIPNNLMPYIAQVAVGRRDSLAIFGNDYPTEDGTGVRDYIHVMDLADGHVVAMEKLANKPGVHIYNLGAGVGNSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYWADASKADRELNWRVTRTLDEMAQDTWHWQSRHPQGYPD 338
                                    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 2UDP)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GALE_ECOLI | P09147)
molecular function
    GO:0070403    NAD+ binding    Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0003978    UDP-glucose 4-epimerase activity    Catalysis of the reaction: UDP-glucose = UDP-galactose.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0009242    colanic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of colanic acid, a capsular bacterial polysaccharide.
    GO:0033499    galactose catabolic process via UDP-galactose    The chemical reactions and pathways resulting in the breakdown of galactose, via the intermediate UDP-galactose.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GALE_ECOLI | P09147: 1a9y 1a9z 1kvq 1kvr 1kvs 1kvt 1kvu 1lrj 1lrk 1lrl 1nah 1nai 1uda 1udb 1udc 1xel 5gy7

(-) Related Entries Specified in the PDB File

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