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(-) Description

Title :  CRYSTAL STRUCTURE OF INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE (TM1347) FROM THERMOTOGA MARITIMA AT 2.18 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  22 Feb 05  (Deposition) - 15 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  B  (4x)
Keywords :  Tm1347, Inosine-5'-Monophosphate Dehydrogenase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Inosine-5'-Monophosphate Dehydrogenase (Tm1347) From Thermotoga Maritima At 2. 18 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.205
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1347
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): A 
Biological Unit 2 (4x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1VRD)

(-) Sites  (0, 0)

(no "Site" information available for 1VRD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:272 -Asn A:273
2Gly B:272 -Asn B:273

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VRD)

(-) 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:321
 aligned with Q9X168_THEMA | Q9X168 from UniProtKB/TrEMBL  Length:482

    Alignment length:457
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       
         Q9X168_THEMA     1 MKEALTFDDVLLVPQYSEVLPKDVKIDTRLTRQIRINIPLVSAAMDTVTEAALAKALAREGGIGIIHKNLTPDEQARQVSIVKKTENGIIYDPITVTPDMTVKEAIDLMAEYKIGGLPVVDEEGRLVGLLTNRDVRFEKNLSKKIKDLMTPREKLIVAPPDISLEKAKEILHQHRIEKLPLVSKDNKLVGLITIKDIMSVIEHPNAARDEKGRLLVGAAVGTSPETMERVEKLVKAGVDVIVIDTAHGHSRRVIETLEMIKADYPDLPVVAGNVATPEGTEALIKAGADAVKVGVGPGSICTTRVVAGVGVPQLTAVMECSEVARKYDVPIIADGGIRYSGDIVKALAAGAESVMVGSIFAGTEEAPGETILYQGRKYKAYRGMGSLGAMRSGSADRYGQEGENKFVPEGIEGMVPYKGTVKDVVHQLVGGLRSGMGYIGARTIKELQEKAVFVKIT 457
               SCOP domains d1vrda1 A:1-85,A:213-457 Inosine monophosphate dehydrogenase (IMPDH)                                                                                                                                ----------------d1vrda1 A:1-85,A:213-457 Inosine monophosphate dehydrogenase (IMPDH)                                                                                                                                                                                  SCOP domains
               CATH domains 1vrdA00 A:1-457 Aldolase class I                                                                                                                                                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhh...eeee....hhhhhhhhhhhhhh.---------------------------------------------------------------------------------------------------------------hhhhhh..............eeee....hhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhh...eeee.......hhhhhhhh...hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh...eeeehhhhhh......eeeee..eeeee....-------------------------.....ee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vrd A   1 MKEALTFDDVLLVPQYSEVLPKDVKIDTRLTRQIRINIPLVSAAMDTVTEAALAKALAREGGIGIIHKNLTPDEQARQVSIVKKT---------------------------------------------------------------------------------------------------------------IMSVIEHPNAARDEKGRLLVGAAVGTSPETMERVEKLVKAGVDVIVIDTAHGHSRRVIETLEMIKADYPDLPVVAGNVATPEGTEALIKAGADAVKVGVGPGSICTTRVVAGVGVPQLTAVMECSEVARKYDVPIIADGGIRYSGDIVKALAAGAESVMVGSIFAGTEEAPGETILYQGRKYKAYRGM-------------------------GIEGMVPYKGTVKDVVHQLVGGLRSGMGYIGARTIKELQEKAVFVKIT 457
                                    10        20        30        40        50        60        70        80    |    -         -         -         -         -         -         -         -         -         -         -      |200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380   |     -         -       410       420       430       440       450       
                                                                                                               85                                                                                                             197                                                                                                                                                                                        384                       410                                               


Chain B from PDB  Type:PROTEIN  Length:317
 aligned with Q9X168_THEMA | Q9X168 from UniProtKB/TrEMBL  Length:482

    Alignment length:457
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       
         Q9X168_THEMA     1 MKEALTFDDVLLVPQYSEVLPKDVKIDTRLTRQIRINIPLVSAAMDTVTEAALAKALAREGGIGIIHKNLTPDEQARQVSIVKKTENGIIYDPITVTPDMTVKEAIDLMAEYKIGGLPVVDEEGRLVGLLTNRDVRFEKNLSKKIKDLMTPREKLIVAPPDISLEKAKEILHQHRIEKLPLVSKDNKLVGLITIKDIMSVIEHPNAARDEKGRLLVGAAVGTSPETMERVEKLVKAGVDVIVIDTAHGHSRRVIETLEMIKADYPDLPVVAGNVATPEGTEALIKAGADAVKVGVGPGSICTTRVVAGVGVPQLTAVMECSEVARKYDVPIIADGGIRYSGDIVKALAAGAESVMVGSIFAGTEEAPGETILYQGRKYKAYRGMGSLGAMRSGSADRYGQEGENKFVPEGIEGMVPYKGTVKDVVHQLVGGLRSGMGYIGARTIKELQEKAVFVKIT 457
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1vrdB00 B:1-457 Aldolase class I                                                                                                                                                                                                                                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) --IMPDH-1vrdB01 B:3-457                                                                                                                                                                                                                                                                                                                                                                                                                                                   Pfam domains (1)
           Pfam domains (2) --IMPDH-1vrdB02 B:3-457                                                                                                                                                                                                                                                                                                                                                                                                                                                   Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CBS-1-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CBS-1-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CBS-1-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CBS-1-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (6)
         Sec.struct. author .....hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhh...eeee....hhhhhhhhhhhhh-------------------------------------------------------------------------------------------------------------------hhhhh.............eeee....hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhh...eeee.......hhhhhhhh...hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhh...eeeehhhhhh......eeeee..eeeeeeee.-------------------------.eeeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vrd B   1 MKEALTFDDVLLVPQYSEVLPKDVKIDTRLTRQIRINIPLVSAAMDTVTEAALAKALAREGGIGIIHKNLTPDEQARQVSIVK-------------------------------------------------------------------------------------------------------------------SVIEHPNAARDEKGRLLVGAAVGTSPETMERVEKLVKAGVDVIVIDTAHGHSRRVIETLEMIKADYPDLPVVAGNVATPEGTEALIKAGADAVKVGVGPGSICTTRVVAGVGVPQLTAVMECSEVARKYDVPIIADGGIRYSGDIVKALAAGAESVMVGSIFAGTEEAPGETILYQGRKYKAYRGM-------------------------GIEGMVPYKGTVKDVVHQLVGGLRSGMGYIGARTIKELQEKAVFVKIT 457
                                    10        20        30        40        50        60        70        80  |      -         -         -         -         -         -         -         -         -         -         -       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380   |     -         -       410       420       430       440       450       
                                                                                                             83                                                                                                                 199                                                                                                                                                                                      384                       410
   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  (1, 2)

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

(-) Pfam Domains  (2, 6)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)
(-)
Clan: no clan defined [family: CBS] (51)
(-)
Family: CBS (51)
(-)
Thermotoga maritima (3)
2aCBS-1vrdB03B:199-203
2bCBS-1vrdB04B:199-203
2cCBS-1vrdB05B:199-203
2dCBS-1vrdB06B:199-203

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9X168_THEMA | Q9X168)
molecular function
    GO:0003938    IMP dehydrogenase activity    Catalysis of the reaction: inosine 5'-phosphate + NAD+ + H2O = xanthosine 5'-phosphate + NADH + H+.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0006177    GMP biosynthetic process    The chemical reactions and pathways resulting in the formation of GMP, guanosine monophosphate.
    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.
    GO:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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