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(-) Description

Title :  DHFR FROM BACILLUS STEAROTHERMOPHILUS
 
Authors :  H. S. Kim, S. M. Damo, S. Y. Lee, D. Wemmer, J. P. Klinman
Date :  14 Apr 05  (Deposition) - 30 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dhfr, Nadp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. S. Kim, S. M. Damo, S. Y. Lee, D. Wemmer, J. P. Klinman
Structure And Hydride Transfer Mechanism Of A Moderate Thermophilic Dihydrofolate Reductase From Bacillus Stearothermophilus And Comparison To Its Mesophilic And Hyperthermophilic Homologues.
Biochemistry V. 44 11428 2005
PubMed-ID: 16114879  |  Reference-DOI: 10.1021/BI050630J

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    Chains: A, B
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO45Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:111 , HOH A:3522 , HOH A:3548BINDING SITE FOR RESIDUE SO4 A 3482
2AC2SOFTWAREGLY A:43 , ARG A:44 , LYS A:45 , THR A:46 , GLY A:98 , HOH A:3510 , HOH A:3557 , HOH A:3644BINDING SITE FOR RESIDUE SO4 A 3483
3AC3SOFTWARELYS A:32 , ARG A:57 , HOH A:3498BINDING SITE FOR RESIDUE SO4 A 3484
4AC4SOFTWAREPHE B:31 , HOH B:3493BINDING SITE FOR RESIDUE SO4 B 3485
5AC5SOFTWAREPHE A:31 , LEU A:54 , HOH A:3516 , HOH A:3619BINDING SITE FOR RESIDUE SO4 A 3486
6AC6SOFTWAREGLY B:43 , ARG B:44 , LYS B:45 , THR B:46 , GLY B:97 , GLY B:98 , ALA B:99 , GLU B:100BINDING SITE FOR RESIDUE GOL B 1901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZDR)

(-) 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:161
 aligned with Q5KZ26_GEOKA | Q5KZ26 from UniProtKB/TrEMBL  Length:164

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
         Q5KZ26_GEOKA     1 MISHIVAMDENRVIGKDNRLPWHLPADLAYFKRVTMGHAIVMGRKTFEAIGRPLPGRDNVVVTRNRSFRPEGCLVLHSLEEVKQWIASRADEVFIIGGAELFRATMPIVDRLYVTKIFASFPGDTFYPPISDDEWEIVSYTPGGKDEKNPYEHAFIIYERK 161
               SCOP domains d1zdra_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains 1zdrA00 A:1-161 Dihydrofolate Reductase, subunit A                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...eee........hhhhhhhhhhhhh..eeeeehhhhhhhh......eeeee...........eee.hhhhhhhhhhh....eeeeehhhhhhhhhhhh.eeeeeee.......ee........eeeeeeee..........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zdr A   1 MISHIVAMDENRVIGKDNRLPWHLPADLAYFKRVTMGHAIVMGRKTFEAIGRPLPGRDNVVVTGNRSFRPEGCLVLHSLEEVKQWIASRADEVFIIGGAELFRATMPIVDRLYVTKIFASFPGDTFYPPISDDEWEIVSYTPGGKDEKNPYEHAFIIYERK 161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 


Chain B from PDB  Type:PROTEIN  Length:160
 aligned with Q5KZ26_GEOKA | Q5KZ26 from UniProtKB/TrEMBL  Length:164

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
         Q5KZ26_GEOKA     1 MISHIVAMDENRVIGKDNRLPWHLPADLAYFKRVTMGHAIVMGRKTFEAIGRPLPGRDNVVVTRNRSFRPEGCLVLHSLEEVKQWIASRADEVFIIGGAELFRATMPIVDRLYVTKIFASFPGDTFYPPISDDEWEIVSYTPGGKDEKNPYEHAFIIYER 160
               SCOP domains d1zdrb_ B: automated matches                                                                                                                                     SCOP domains
               CATH domains 1zdrB00 B:1-160 Dihydrofolate Reductase, subunit A                                                                                                               CATH domains
           Pfam domains (1) DHFR_1-1zdrB01 B:1-160                                                                                                                                           Pfam domains (1)
           Pfam domains (2) DHFR_1-1zdrB02 B:1-160                                                                                                                                           Pfam domains (2)
         Sec.struct. author .eeeeeeee...eee........hhhhhhhhhhhhh.eeeeehhhhhhh.......eeeee................hhhhhh.........eeeeehhhhhhhhhhhh.eeeeeee.......ee.........eeeeeee..........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zdr B   1 MISHIVAMDENRVIGKDNRLPWHLPADLAYFKRVTMGHAIVMGRKTFEAIGRPLPGRDNVVVTGNRSFRPEGCLVLHSLEEVKQWIASRADEVFIIGGAELFRATMPIVDRLYVTKIFASFPGDTFYPPISDDEWEIVSYTPGGKDEKNPYEHAFIIYER 160
                                    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)
    → 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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: DHFred (95)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5KZ26_GEOKA | Q5KZ26)
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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  1zdr
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