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(-) Description

Title :  THE CRYSTAL STRUCTURE OF TM1154, OXIDOREDUCTASE, SOL/DEVB FAMILY FROM THERMOTOGA MARITIMA
 
Authors :  Y. Kim, A. Joachimiak, A. Edwards, T. Skarina, A. Savchenko, Midwest Center For Structural Genomics (Mcsg)
Date :  15 May 03  (Deposition) - 23 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Alpha-Beta, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, A. Joachimiak, A. Edwards, T. Skarina, A. Savchenko
The Crystal Structure Analysis Of Tm1154, Oxidoreductase From Thermotoga Maritima
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 6-PHOSPHOGLUCONOLACTONASE
    Chains: A
    EC Number: 3.1.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: TM1154 PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2FMT1Ligand/IonFORMIC ACID
3MSE3Mod. Amino AcidSELENOMETHIONINE
4SO42Ligand/IonSULFATE ION
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:70 , HIS A:138 , ALA A:140 , ASP A:162 , ARG A:167 , HOH A:328 , HOH A:363 , HOH A:382 , HOH A:581BINDING SITE FOR RESIDUE SO4 A 302
2AC2SOFTWAREARG A:43 , THR A:44 , LYS A:190 , HOH A:354 , HOH A:581 , HOH A:602BINDING SITE FOR RESIDUE SO4 A 303
3AC3SOFTWAREVAL A:99 , HIS A:100 , TYR A:101 , ASP A:103 , LYS A:114 , GLU A:118 , HOH A:321 , HOH A:330 , HOH A:561BINDING SITE FOR RESIDUE TRS A 301
4AC4SOFTWARELYS A:3 , LYS A:20 , LYS A:213 , HOH A:491 , HOH A:576BINDING SITE FOR RESIDUE EDO A 304
5AC5SOFTWAREILE A:119 , THR A:123 , ASP A:124 , GLN A:125 , PHE A:126 , THR A:177 , HOH A:531BINDING SITE FOR RESIDUE FMT A 305

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:162 -Pro A:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PBT)

(-) 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:220
 aligned with 6PGL_THEMA | Q9X0N8 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
           6PGL_THEMA     1 MEKTVIYLLEDGYVDFVVEKIRTKMEKLLEEKDKIFVVLAGGRTPLPVYEKLAEQKFPWNRIHFFLSDERYVPLDSDQSNFRNINEVLFSRAKIPSGNVHYVDTSLPIEKACEKYEREIRSATDQFDLAILGMGPDGHVASIFDLETGNKDNLVTFTDPSGDPKVPRVTLTFRALNTSLYVLFLIRGKEKINRLTEILKDTPLPAYFVRGKEKTVWFVGK 220
               SCOP domains d1pbta_ A: 6-phosphogluconolactonase                                                                                                                                                                                         SCOP domains
               CATH domains -1pbtA00 A:2-220  [code=3.40.50.1360, no name defined]                                                                                                                                                                       CATH domains
               Pfam domains ------------Glucosamine_iso-1pbtA01 A:13-199                                                                                                                                                           --------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhh....hhh.eeeee.eee........hhhhhhhhhh......hhh.ee......hhhhhhhhhhhhhhhhh....eeee............hhhhhh....eee..........eeeehhhhhh...eeeeeeehhhhhhhhhhhhh...hhhhhh....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pbt A   1 mEKTVIYLLEDGYVDFVVEKIRTKmEKLLEEKDKIFVVLAGGRTPLPVYEKLAEQKFPWNRIHFFLSDERYVPLDSDQSNFRNINEVLFSRAKIPSGNVHYVDTSLPIEKACEKYEREIRSATDQFDLAILGmGPDGHVASIFDLETGNKDNLVTFTDPSGDPKVPRVTLTFRALNTSLYVLFLIRGKEKINRLTEILKDTPLPAYFVRGKEKTVWFVGK 220
                            |       10        20    |   30        40        50        60        70        80        90       100       110       120       130  |    140       150       160       170       180       190       200       210       220
                            |                      25-MSE                                                                                                     133-MSE                                                                                   
                            1-MSE
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: ISOCOT_Fold (53)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (6PGL_THEMA | Q9X0N8)
molecular function
    GO:0017057    6-phosphogluconolactonase activity    Catalysis of the reaction: 6-O-phosphono-D-glucono-1,5-lactone + H(2)O = 6-phospho-D-gluconate + H(+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
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:0006098    pentose-phosphate shunt    The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.

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 Related Entries

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        6PGL_THEMA | Q9X0N8: 1vl1

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