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(-) Description

Title :  DIHYDROFOLATE REDUCTASE FROM THERMOTOGA MARITIMA
 
Authors :  T. Dams, G. Auerbach, G. Bader, T. Ploom, R. Huber, R. Jaenicke
Date :  16 Sep 99  (Deposition) - 31 Mar 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dimer, Hyperthermophile, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Dams, G. Auerbach, G. Bader, U. Jacob, T. Ploom, R. Huber, R. Jaenicke
The Crystal Structure Of Dihydrofolate Reductase From Thermotoga Maritima: Molecular Features Of Thermostability.
J. Mol. Biol. V. 297 659 2000
PubMed-ID: 10731419  |  Reference-DOI: 10.1006/JMBI.2000.3570
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    Chains: A, B
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTD(TRC)
    Expression System Taxid: 562
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Other Details: GENOMIC LIBRARY

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MTX2Ligand/IonMETHOTREXATE
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:7 , ALA A:8 , ILE A:15 , ALA A:16 , GLY A:44 , ARG A:45 , ILE A:46 , THR A:47 , GLU A:50 , LEU A:63 , THR A:64 , ARG A:65 , ARG A:66 , GLY A:80 , ILE A:100 , GLY A:101 , GLY A:102 , LYS A:103 , THR A:104 , GLU A:108 , ILE A:131 , MTX A:171 , HOH A:534 , HOH A:556 , HOH A:580BINDING SITE FOR RESIDUE NDP A 170
2AC2SOFTWAREVAL A:6 , LEU A:7 , ALA A:8 , ASP A:27 , ARG A:28 , LYS A:29 , PHE A:31 , ARG A:32 , GLU A:50 , ILE A:51 , ARG A:53 , LEU A:55 , ARG A:58 , ILE A:100 , THR A:121 , NDP A:170 , HOH A:502BINDING SITE FOR RESIDUE MTX A 171
3AC3SOFTWARELEU B:7 , ALA B:8 , ILE B:15 , GLY B:44 , ARG B:45 , ILE B:46 , THR B:47 , GLU B:50 , LEU B:63 , THR B:64 , ARG B:65 , ARG B:66 , GLY B:80 , ILE B:100 , GLY B:101 , GLY B:102 , LYS B:103 , THR B:104 , GLU B:108 , ILE B:131 , MTX B:171 , HOH B:641BINDING SITE FOR RESIDUE NDP B 170
4AC4SOFTWAREVAL B:6 , LEU B:7 , ALA B:8 , ASP B:27 , ARG B:28 , PHE B:31 , ARG B:32 , GLU B:50 , ILE B:51 , ARG B:53 , LEU B:55 , ARG B:58 , ILE B:100 , THR B:121 , NDP B:170 , HOH B:503 , HOH B:571BINDING SITE FOR RESIDUE MTX B 171

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D1G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1D1G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D1G)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHFR_2PS51330 Dihydrofolate reductase (DHFR) domain profile.DYR_THEMA3-169
 		  2A:2-164
B:2-164

(-) Exons   (0, 0)

(no "Exon" information available for 1D1G)

(-) 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:164
 aligned with DYR_THEMA | Q60034 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
            DYR_THEMA     2 AKVIFVLAMDVSGKIASSVESWSSFEDRKNFRKITTEIGNVVMGRITFEEIGRPLPERLNVVLTRRPKTSNNPSLVFFNGSPADVVKFLEGKGYERVAVIGGKTVFTEFLREKLVDELFVTVEPYVFGKGIPFFDEFEGYFPLKLLEMRRLNERGTLFLKYSVE 165
               SCOP domains d1d1ga_ A: Dihydrofolate reductase, prokaryotic type                                                                                                                 SCOP domains
               CATH domains 1d1gA00 A:1-164 Dihydrofolate Reductase, subunit A                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eee.......hhhhhhhhhhhhhhhheeeeehhhhhhhh......eeeee...........eeee..hhhhhhhhhhh....eeeeeehhhhhhhhhhh....eeeeee..eee...ee.......eeeeeeeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -DHFR_2  PDB: A:2-164 UniProt: 3-169                                                                                                                                 PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d1g A   1 AKVIFVLAMDVSGKIASSVESWSSFEDRKNFRKITTEIGNVVMGRITFEEIGRPLPERLNVVLTRRPKTSNNPSLVFFNGSPADVVKFLEGKGYERVAVIGGKTVFTEFLREKLVDELFVTVEPYVFGKGIPFFDEFEGYFPLKLLEMRRLNERGTLFLKYSVE 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    


Chain B from PDB  Type:PROTEIN  Length:164
 aligned with DYR_THEMA | Q60034 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
            DYR_THEMA     2 AKVIFVLAMDVSGKIASSVESWSSFEDRKNFRKITTEIGNVVMGRITFEEIGRPLPERLNVVLTRRPKTSNNPSLVFFNGSPADVVKFLEGKGYERVAVIGGKTVFTEFLREKLVDELFVTVEPYVFGKGIPFFDEFEGYFPLKLLEMRRLNERGTLFLKYSVE 165
               SCOP domains d1d1gb_ B: Dihydrofolate reductase, prokaryotic type                                                                                                                 SCOP domains
               CATH domains 1d1gB00 B:1-164 Dihydrofolate Reductase, subunit A                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eee.......hhhhhhhhhhhhhhhheeeeehhhhhhhh......eeeee...........eeee..hhhhhhhhhhh....eeeeeehhhhhhhhhhh....eeeeee..eee...ee.......eeeeeeeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -DHFR_2  PDB: B:2-164 UniProt: 3-169                                                                                                                                 PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d1g B   1 AKVIFVLAMDVSGKIASSVESWSSFEDRKNFRKITTEIGNVVMGRITFEEIGRPLPERLNVVLTRRPKTSNNPSLVFFNGSPADVVKFLEGKGYERVAVIGGKTVFTEFLREKLVDELFVTVEPYVFGKGIPFFDEFEGYFPLKLLEMRRLNERGTLFLKYSVE 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D1G)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DYR_THEMA | Q60034)
molecular function
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0004146    dihydrofolate reductase activity    Catalysis of the reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+.
    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:0006545    glycine biosynthetic process    The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
    GO:0009165    nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    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:0046654    tetrahydrofolate biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.

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 Related Entries

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        DYR_THEMA | Q60034: 1cz3

(-) Related Entries Specified in the PDB File

1cz3 UNLIGANDED ENZYME FROM THE SAME SPECIES