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(-) Description

Title :  CRYSTAL STRUCTURE OF UDP-GALACTOSE 4-EPIMERASE
 
Authors :  H. Sakuraba, T. Kawai, K. Yoneda, T. Ohshima
Date :  18 Jul 09  (Deposition) - 21 Jul 10  (Release) - 21 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rossmann Fold, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Sakuraba, T. Kawai, K. Yoneda, T. Ohshima
Crystal Structure Of Udp-Galactose 4-Epimerase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NAD-DEPENDENT EPIMERASE/DEHYDRATASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROBACULUM CALIDIFONTIS
    Organism Taxid: 410359
    Strain: JCM 11548
    Synonym: UDP-GALACTOSE 4-EPIMERASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:7 , ALA A:9 , GLY A:10 , PHE A:11 , ILE A:12 , ASP A:31 , ASN A:32 , SER A:34 , SER A:35 , GLY A:36 , ARG A:50 , ASP A:51 , LEU A:52 , PHE A:69 , ALA A:70 , ALA A:71 , PRO A:73 , GLU A:74 , GLU A:88 , ALA A:111 , SER A:112 , TYR A:137 , LYS A:141 , TYR A:164 , ALA A:165 , ASN A:166 , VAL A:167 , HIS A:174 , HOH A:315 , HOH A:318 , HOH A:356 , HOH A:357 , HOH A:369BINDING SITE FOR RESIDUE NAD A 901
2AC2SOFTWAREHIS A:48 , ARG A:50 , HOH A:344 , HOH A:427BINDING SITE FOR RESIDUE PO4 A 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile A:123 -Pro A:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ICP)

(-) 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:295
 aligned with A3MUJ4_PYRCJ | A3MUJ4 from UniProtKB/TrEMBL  Length:312

    Alignment length:311
                                    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 
         A3MUJ4_PYRCJ     1 MRIVVTGGAGFIGSHLVDKLVELGYEVVVVDNLSSGRREFVNPSAELHVRDLKDYSWGAGIKGDVVFHFAANPEVRLSTTEPIVHFNENVVATFNVLEWARQTGVRTVVFASSSTVYGDADVIPTPEEEPYKPISVYGAAKAAGEVMCATYARLFGVRCLAVRYANVVGPRLRHGVIYDFIMKLRRNPNVLEVLGDGTQRKSYLYVRDAVEATLAAWKKFEEMDAPFLALNVGNVDAVRVLDIAQIVAEVLGLRPEIRLVPSTPDGRGWPGDVKYMTLAVTKLMKLTGWRPTMTSAEAVKKTAEDLAKELW 311
               SCOP domains d3icpa_ A: automated matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh..eeeee......hhhhh....eee................eeee............hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee......hhhhhhhhhhhhh..ee.------.ee.eeehhhhhhhhhhhhhhhhh....eeeeee.....eehhhhhhhhhhhh....ee...----------....ee...hhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3icp A   1 MRIVVTGGAGFIGSHLVDKLVELGYEVVVVDNLSSGRREFVNPSAELHVRDLKDYSWGAGIKGDVVFHFAANPEVRLSTTEPIVHFNENVVATFNVLEWARQTGVRTVVFASSSTVYGDADVIPTPEEEPYKPISVYGAAKAAGEVMCATYARLFGVRCLAVRYANVVGPRLRHGVIYDFIMKLRRNPNVLE------QRKSYLYVRDAVEATLAAWKKFEEMDAPFLALNVGNVDAVRVLDIAQIVAEVLGLRPEIRLV----------GDVKYMTLAVTKLMKLTGWRPTMTSAEAVKKTAEDLAKELW 311
                                    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         -|      280       290       300       310 
                                                                                                                                                                                                                         192    199                                                          260        271
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "CATH Domain" information available for 3ICP)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (A3MUJ4_PYRCJ | A3MUJ4)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050662    coenzyme binding    Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
    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.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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        A3MUJ4_PYRCJ | A3MUJ4: 3aw9 3ko8

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