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(-) Description

Title :  UDP-GALACTOSE 4-EPIMERASE FROM ESCHERICHIA COLI
 
Authors :  J. Thoden, H. Holden
Date :  25 Jan 96  (Deposition) - 12 Feb 97  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Thoden, P. A. Frey, H. M. Holden
Molecular Structure Of The Nadh/Udp-Glucose Abortive Comple Of Udp-Galactose 4-Epimerase From Escherichia Coli: Implications For The Catalytic Mechanism.
Biochemistry V. 35 5137 1996
PubMed-ID: 8611497  |  Reference-DOI: 10.1021/BI9601114

(-) Compounds

Molecule 1 - UDP-GALACTOSE 4-EPIMERASE
    Chains: A
    EC Number: 5.1.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7E2
    Expression System Strain: BL21 (DE3), PLYSS
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: NADH/UDP-GLUCOSE ABORTIVE COMPLEX

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric Unit (5, 6)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2NA2Ligand/IonSODIUM ION
3NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5UPG1Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2NA-1Ligand/IonSODIUM ION
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5UPG2Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:91 , HOH A:392 , HOH A:393 , HOH A:534 , HOH A:616 , HOH A:749BINDING SITE FOR RESIDUE NA A 352
2AC2SOFTWAREGLN A:334 , HOH A:542 , HOH A:545 , HOH A:546 , HOH A:596BINDING SITE FOR RESIDUE NA A 353
3AC3SOFTWAREGLY 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 , TYR A:149 , LYS A:153 , TYR A:177 , PRO A:180 , UPG A:341 , EDO A:351 , HOH A:355 , HOH A:379 , HOH A:382 , HOH A:411 , HOH A:514BINDING SITE FOR RESIDUE NAD A 340
4AC4SOFTWARESER A:124 , THR A:126 , TYR A:149 , PHE A:178 , ASN A:179 , ASN A:198 , ASN A:199 , LEU A:200 , LEU A:215 , 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 , TYR A:299 , NAD A:340 , HOH A:414 , HOH A:428 , HOH A:499 , HOH A:501 , HOH A:527 , HOH A:549 , HOH A:570 , HOH A:597 , HOH A:724BINDING SITE FOR RESIDUE UPG A 341
5AC5SOFTWARETYR A:11 , ASN A:35 , GLY A:190 , ASP A:192 , NAD A:340 , HOH A:356 , HOH A:421BINDING SITE FOR RESIDUE EDO A 351
6AC6SOFTWARELEU A:250 , LYS A:253 , TYR A:259 , GLU A:309 , HOH A:614BINDING SITE FOR RESIDUE PEG A 354

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile A:134 -Pro A:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XEL)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XEL)

(-) 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: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 d1xela_ A: Uridine diphosphogalactose-4-epimerase (UDP-galactose 4-epimerase)                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1xelA02 A:1-181,A:232-262 NAD(P)-binding Rossmann-like Domain                                                                                                                        1xelA01 A:182-231,A:263-338                       1xelA02 A:1-181,A:232-262      1xelA01 A:182-231,A:263-338 UDP-galactose 4-epimerase, domain 1              CATH domains
               Pfam domains --Epimerase-1xelA01 A:3-262                                                                                                                                                                                                                                           ------------Epimerase_Csub-1xelA02 A:275-336                              -- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhh..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
                 1xel A   1 MRVLVTGGSGYIGSHTCVQLLQNGHDVIILDNLCNSKRSVLPVIERLGGKHPTFVEGDIRNEALMTEILHDHAIDTVIHFAGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNFIFSSSATVYGDNPKIPYVESFPTGTPQSPYGKSKLMVEQILTDLQKAQPDWSIALLRYFNPVGAHPSGDMGEDPQGIPNNLMPYIAQVAVGRRDSLAIFGNDYPTEDGTGVRDYIHVMDLADGHVVAMEKLANKPGVHIYNLGAGVGNSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYWADASKADRELNWRVTRTLDEMAQDTWHWQSRHPQGYPD 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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: Epimerase_Csub] (12)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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UniProtKB/Swiss-Prot
        GALE_ECOLI | P09147: 1a9y 1a9z 1kvq 1kvr 1kvs 1kvt 1kvu 1lrj 1lrk 1lrl 1nah 1nai 1uda 1udb 1udc 2udp 5gy7

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