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(-) Description

Title :  CRYSTAL STRUCTURE OF A 'HUMANIZED' E. COLI DIHYDROFOLATE REDUCTASE
 
Authors :  J. B. French, C. T. Liu, P. Hanoian, T. H. Pringle, S. Hammes-Schiffer, S. J. Benkovic
Date :  07 Aug 12  (Deposition) - 05 Jun 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Keywords :  Tetrahydrofolate, Enzyme Catalysis, Evolution, Dihydrofolate Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. T. Liu, P. Hanoian, J. B. French, T. H. Pringle, S. Hammes-Schiffer, S. J. Benkovic
Functional Significance Of Evolving Protein Sequence In Dihydrofolate Reductase From Bacteria To Humans.
Proc. Natl. Acad. Sci. Usa V. 110 10159 2013
PubMed-ID: 23733948  |  Reference-DOI: 10.1073/PNAS.1307130110

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    Chains: B, A
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FOLA, TMRA, B0048, JW0047
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2MTX2Ligand/IonMETHOTREXATE
3NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MTX1Ligand/IonMETHOTREXATE
3NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MTX1Ligand/IonMETHOTREXATE
3NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE B:5 , ALA B:6 , ALA B:7 , MET B:20 , ASP B:28 , LEU B:29 , PHE B:32 , LYS B:33 , SER B:50 , ASN B:55 , ARG B:61 , ILE B:98 , TYR B:104 , THR B:117 , NDP B:202 , HOH B:303 , HOH B:318 , HOH B:330 , HOH B:366BINDING SITE FOR RESIDUE MTX B 201
2AC2SOFTWAREALA B:6 , ALA B:7 , ILE B:14 , GLY B:15 , ASN B:18 , ALA B:19 , GLY B:44 , ARG B:45 , HIS B:46 , THR B:47 , LEU B:66 , SER B:67 , SER B:68 , LYS B:80 , ILE B:98 , GLY B:100 , GLY B:101 , ARG B:102 , VAL B:103 , TYR B:104 , GLN B:106 , MTX B:201 , HOH B:302 , HOH B:312 , HOH B:335 , HOH B:339 , HOH B:340 , HOH B:353BINDING SITE FOR RESIDUE NDP B 202
3AC3SOFTWAREGLU B:53 , ARG B:56 , HOH B:365BINDING SITE FOR RESIDUE CA B 203
4AC4SOFTWAREILE A:5 , ALA A:6 , MET A:20 , ASP A:28 , PHE A:32 , LYS A:33 , ASN A:55 , ARG A:61 , ILE A:98 , TYR A:104 , THR A:117 , NDP A:202 , HOH A:305 , HOH A:360 , HOH A:395BINDING SITE FOR RESIDUE MTX A 201
5AC5SOFTWAREALA A:6 , ALA A:7 , ILE A:14 , GLY A:15 , ASN A:18 , ALA A:19 , GLY A:44 , ARG A:45 , HIS A:46 , THR A:47 , LEU A:66 , SER A:67 , SER A:68 , LYS A:80 , ILE A:98 , GLY A:100 , GLY A:101 , ARG A:102 , VAL A:103 , TYR A:104 , GLN A:106 , MTX A:201 , HOH A:303 , HOH A:321 , HOH A:330 , HOH A:343 , HOH A:357 , HOH A:364 , HOH A:384BINDING SITE FOR RESIDUE NDP A 202
6AC6SOFTWAREASP A:131 , GLU A:133 , HOH A:354 , HOH A:355BINDING SITE FOR RESIDUE CA A 203
7AC7SOFTWAREGLU A:53 , ARG A:56 , HOH A:370BINDING SITE FOR RESIDUE CA A 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GH8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg B:56 -Pro B:57
2Gly B:99 -Gly B:100
3Arg A:56 -Pro A:57
4Gly A:99 -Gly A:100

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GH8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GH8)

(-) Exons   (0, 0)

(no "Exon" information available for 4GH8)

(-) 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:162
                                                                                                                                                                                                  
               SCOP domains d4gh8a_ A: Dihydrofolate reductase, prokaryotic type                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeehhh.eee.........hhhhhhhhhhhhh..eeeeehhhhhhhhhhhh.....eeeee..........eee.hhhhhhhhhh....eee..hhhhhhhhhhhh.eeeeeee.......ee.........eeeeeeee.........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gh8 A   1 MISLIAALAVDRVIGMENAMPWPPLPADLAWFKRNTLNKPVIMGRHTWESIPEKNRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILER 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  


Chain B from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains d4gh8b_ B: Dihydrofolate reductase, prokaryotic type                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeehhh.eee.........hhhhhhhhhhhhh...eeeehhhhhhhhhhhh......eeee..........eee.hhhhhhhhhh....eee..hhhhhhhhhhhh.eeeeeee.......ee.........eeeeeeee.........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gh8 B   1 MISLIAALAVDRVIGMENAMPWPPLPADLAWFKRNTLNKPVIMGRHTWESIPEKNRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILER 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   Legend:   → Mismatch (orange background)
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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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GH8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GH8)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

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        DYR_ECOLI | P0ABQ4: 1ddr 1dds 1dhi 1dhj 1dra 1drb 1dre 1drh 1dyh 1dyi 1dyj 1jol 1jom 1ra1 1ra2 1ra3 1ra8 1ra9 1rb2 1rb3 1rc4 1rd7 1re7 1rf7 1rg7 1rh3 1rx1 1rx2 1rx3 1rx4 1rx5 1rx6 1rx7 1rx8 1rx9 1tdr 2ano 2anq 2d0k 2drc 2inq 3dau 3drc 3k74 3kfy 3och 3ql3 3qyl 3qyo 3r33 4dfr 4eig 4eiz 4ej1 4fhb 4i13 4i1n 4kjj 4kjk 4kjl 4nx6 4nx7 4pdj 4x5f 4x5g 4x5h 4x5i 4x5j 5cc9 5ccc 5dfr 5e8q 5eaj 6dfr 7dfr

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