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(-) Description

Title :  CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS HB8 UDP-GLUCOSE 4-EPIMERASE COMPLEX WITH NAD
 
Authors :  Z-Q. Fu, L. Chen, A. Ebihara, A. Shinkai, S. Kuramitsu, S. Yokoyama, J. Zhu, J. T. Swindell, J. Chrzas, J. P. Rose, B-C. Wang, Southeast Collaboratory For Structural Genomics (Secsg), Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  16 Mar 07  (Deposition) - 17 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym./Biol. Unit :  A
Keywords :  Ttha0591, Structural Genomics, Udp-Glucose 4-Epimerase, Thermus Thermophilus Hb8, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z-Q. Fu, L. Chen, A. Ebihara, A. Shinkai, S. Kuramitsu, S. Yokoyama, J. Zhu, J. T. Swindell, J. Chrzas, J. P. Rose, B-C. Wang
Crystal Structure Of Thermus Thermophilus Hb8 Udp-Glucose 4-Epimerase Complex With Nad
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UDP-GLUCOSE 4-EPIMERASE
    Atcc: 27634
    Chains: A
    EC Number: 5.1.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TTHA0591
    Organism Scientific: THERMUS THERMOPHILUS HB8
    Organism Taxid: 300852
    Strain: HB8, DSM 579

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:7 , ALA A:9 , GLY A:10 , PHE A:11 , ILE A:12 , ASP A:31 , ASN A:32 , LEU A:33 , ALA A:34 , THR A:35 , GLY A:36 , VAL A:50 , ASP A:51 , LEU A:52 , GLN A:73 , ALA A:74 , ALA A:75 , ALA A:77 , VAL A:92 , ALA A:115 , SER A:116 , TYR A:143 , LYS A:147 , TYR A:170 , GLY A:171 , VAL A:173 , GLU A:183 , ALA A:184 , HOH A:1120 , HOH A:1123 , HOH A:1127 , HOH A:1154 , HOH A:1261BINDING SITE FOR RESIDUE NAD A 1118

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P5Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P5Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P5Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P5Y)

(-) Exons   (0, 0)

(no "Exon" information available for 2P5Y)

(-) 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:311
 aligned with Q5SKQ2_THET8 | Q5SKQ2 from UniProtKB/TrEMBL  Length:311

    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 
         Q5SKQ2_THET8     1 MRVLVTGGAGFIGSHIVEDLLARGLEVAVLDNLATGKRENVPKGVPFFRVDLRDKEGVERAFREFRPTHVSHQAAQASVKVSVEDPVLDFEVNLLGGLNLLEACRQYGVEKLVFASTGGAIYGEVPEGERAEETWPPRPKSPYAASKAAFEHYLSVYGQSYGLKWVSLRYGNVYGPRQDPHGEAGVVAIFAERVLKGLPVTLYARKTPGDEGCVRDYVYVGDVAEAHALALFSLEGIYNVGTGEGHTTREVLMAVAEAAGKAPEVQPAPPRPGDLERSVLSPLKLMAHGWRPKVGFQEGIRLTVDHFRGAV 311
               SCOP domains d2p5ya_ A: automated matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2p5yA01 A:1-174,A:216-241 NAD(P)-binding Rossmann-like Domain                                                                                                                 2p5yA02 A:175-215,A:242-311              2p5yA01 A:1-174,A:216-241 2p5yA02 A:175-215,A:242-311 UDP-galactose 4-epimerase, domain 1        CATH domains
               Pfam domains --Epimerase-2p5yA01 A:3-241                                                                                                                                                                                                                      ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhh...eeeee......hhhhh.....ee.....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhh.................hhhhhhhhhhhhhhhhhhhhhh..eeeeee.eee.........hhhhhhhhhhhhhh..eeee..........ee.eeehhhhhhhhhhhhhhh.eeeee.....eehhhhhhhhhhhhh....eeee.............hhhhhh.......hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p5y A   1 MRVLVTGGAGFIGSHIVEDLLARGLEVAVLDNLATGKRENVPKGVPFFRVDLRDKEGVERAFREFRPTHVSHQAAQASVKVSVEDPVLDFEVNLLGGLNLLEACRQYGVEKLVFASTGGAIYGEVPEGERAEETWPPRPKSPYAASKAAFEHYLSVYGQSYGLKWVSLRYGNVYGPRQDPHGEAGVVAIFAERVLKGLPVTLYARKTPGDEGCVRDYVYVGDVAEAHALALFSLEGIYNVGTGEGHTTREVLMAVAEAAGKAPEVQPAPPRPGDLERSVLSPLKLMAHGWRPKVGFQEGIRLTVDHFRGAV 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
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5SKQ2_THET8 | Q5SKQ2)
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.

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(-) Related Entries Specified in the PDB File

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