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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C707S MUTANT OF C-TERMINAL DOMAIN OF 10'FORMYLTETRAHYDROFOLATE DEHYDROGENASE IN COMPLEX WITH NADPH
 
Authors :  Y. Tsybovsky
Date :  17 Aug 12  (Deposition) - 23 Jan 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.38
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Aldehyde Dehydrogenase, Fdh, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Tsybovsky, Y. Malakhau, K. C. Strickland, S. A. Krupenko
The Mechanism Of Discrimination Between Oxidized And Reduce Coenzyme In The Aldehyde Dehydrogenase Domain Of Aldh1L1.
Chem. Biol. Interact V. 202 62 2013
PubMed-ID: 23295222  |  Reference-DOI: 10.1016/J.CBI.2012.12.015

(-) Compounds

Molecule 1 - CYTOSOLIC 10-FORMYLTETRAHYDROFOLATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.5.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: C-TERMINAL DOMAIN, RESIDUES 397-902
    Gene: ALDH1L1, FTHFD
    Mutation: YES
    Organism Common: BROWN RAT,RAT,RATS
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: 10-FTHFDH, FDH, ALDEHYDE DEHYDROGENASE FAMILY 1 MEMBER L1, FBP-CI

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:570 , ILE A:571 , PRO A:572 , TRP A:573 , ASN A:574 , MET A:579 , LYS A:597 , ALA A:599 , GLN A:600 , SER A:629 , GLY A:630 , GLY A:634 , GLN A:635 , PHE A:648 , THR A:649 , GLY A:650 , SER A:651 , VAL A:654 , ILE A:658 , GLU A:673 , LEU A:674 , GLY A:675 , SER A:707 , GLU A:804 , PHE A:806 , LEU A:834 , PHE A:872BINDING SITE FOR RESIDUE NDP A 1001
2AC2SOFTWAREILE B:571 , TRP B:573 , ASN B:574 , LYS B:597 , GLN B:600 , SER B:629 , GLY B:630 , GLY B:634 , GLN B:635 , PHE B:648 , THR B:649 , GLY B:650 , SER B:651 , VAL B:654 , ILE B:658 , GLU B:673 , LEU B:674 , GLY B:675 , SER B:707 , GLU B:804 , PHE B:806 , LEU B:834 , PHE B:872BINDING SITE FOR RESIDUE NDP B 1001
3AC3SOFTWAREVAL C:570 , ILE C:571 , PRO C:572 , TRP C:573 , ASN C:574 , LYS C:597 , ALA C:599 , GLN C:600 , GLY C:630 , GLY C:634 , GLN C:635 , PHE C:648 , THR C:649 , GLY C:650 , SER C:651 , VAL C:654 , HIS C:657 , ILE C:658 , GLU C:673 , LEU C:674 , GLY C:675 , SER C:707 , GLU C:804 , PHE C:806 , LEU C:834 , PHE C:872BINDING SITE FOR RESIDUE NDP C 1001
4AC4SOFTWAREVAL D:570 , ILE D:571 , TRP D:573 , ASN D:574 , LYS D:597 , ALA D:599 , GLN D:600 , SER D:629 , GLY D:630 , GLY D:634 , GLN D:635 , PHE D:648 , THR D:649 , GLY D:650 , SER D:651 , VAL D:654 , ILE D:658 , GLU D:673 , LEU D:674 , GLY D:675 , SER D:707 , GLU D:804 , PHE D:806 , LEU D:834 , PHE D:872BINDING SITE FOR RESIDUE NDP D 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GO0)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Arg A:551 -Pro A:552
2Arg B:551 -Pro B:552
3Arg C:551 -Pro C:552
4Arg D:551 -Pro D:552

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GO0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GO0)

(-) Exons   (0, 0)

(no "Exon" information available for 4GO0)

(-) 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:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee..eeeeee..eee..eee.hhhh.eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhh...ee........eeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh.....eee...hhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh...eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh..eeee..............eeee.....hhhhhh.....eeeeeee....hhhhhhhhhh.......eee..hhhhhhhhhhhh...eeee..............hhh.ee....hhhhhhh.eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4go0 A 405 VINYVEKAVNKLTLQMPYQLFIGGEFVDAEGSKTYNTINPTDGSVICQVSLAQVSDVDKAVAAAKEAFENGLWGKINARDRGRLLYRLADVMEQHQEELATIEALDAGAVYTLALKTHVGMSIQTFRYFAGWCDKIQGATIPINQARPNRNLTLTKKEPVGVCGIVIPWNYPLMMLSWKTAACLAAGNTVVIKPAQVTPLTALKFAELTLKAGIPKGVVNILPGSGSLVGQRLSDHPDVRKIGFTGSTEVGKHIMKSCALSNVKKVSLELGGKSPLIIFADCDLNKAVQMGMSSVFFNKGENSIAAGRLFVEESIHNQFVQKVVEEVEKMKIGNPLERDTNHGPQNHEAHLRKLVEYCQRGVKEGATLVCGGNQVPRPGFFFQPTVFTDVEDHMYIAKEESFGPIMIISRFADGDVDAVLSRANATEFGLASGVFTRDINKALYVSDKLQAGTVFINTYNKTDVAAPFGGFKQSGFGKDLGEAALNEYLRIKTVTFEY 902
                                   414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894        


Chain B from PDB  Type:PROTEIN  Length:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee....eeee...eee..eee.hhhh.eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhhhh..ee.........eeeeeeeeee...eeee....hhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhh.....eee......hhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhh.eeeee.....eeee....hhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh.eeee..............eeee.....hhhhhh.....eeeeeee...hhhhhhhhhh.......eeee..hhhhhhhhhhhh...eeee..............hhhhh.....hhhhhhh.eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4go0 B 405 VINYVEKAVNKLTLQMPYQLFIGGEFVDAEGSKTYNTINPTDGSVICQVSLAQVSDVDKAVAAAKEAFENGLWGKINARDRGRLLYRLADVMEQHQEELATIEALDAGAVYTLALKTHVGMSIQTFRYFAGWCDKIQGATIPINQARPNRNLTLTKKEPVGVCGIVIPWNYPLMMLSWKTAACLAAGNTVVIKPAQVTPLTALKFAELTLKAGIPKGVVNILPGSGSLVGQRLSDHPDVRKIGFTGSTEVGKHIMKSCALSNVKKVSLELGGKSPLIIFADCDLNKAVQMGMSSVFFNKGENSIAAGRLFVEESIHNQFVQKVVEEVEKMKIGNPLERDTNHGPQNHEAHLRKLVEYCQRGVKEGATLVCGGNQVPRPGFFFQPTVFTDVEDHMYIAKEESFGPIMIISRFADGDVDAVLSRANATEFGLASGVFTRDINKALYVSDKLQAGTVFINTYNKTDVAAPFGGFKQSGFGKDLGEAALNEYLRIKTVTFEY 902
                                   414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894        


Chain C from PDB  Type:PROTEIN  Length:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee..eeeee...eee..eee.hhhh.eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhh...ee........eeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh......eee......hhhhhhhhh....eeeee.hhhhhhhhhhhhhhh...eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh..eeee...ee.....ee..eeee.....hhhhhh.....eeeeeee....hhhhhhhhh........eee..hhhhhhhhhhhh...eeee..............hhhhh.....hhhhh...eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4go0 C 405 VINYVEKAVNKLTLQMPYQLFIGGEFVDAEGSKTYNTINPTDGSVICQVSLAQVSDVDKAVAAAKEAFENGLWGKINARDRGRLLYRLADVMEQHQEELATIEALDAGAVYTLALKTHVGMSIQTFRYFAGWCDKIQGATIPINQARPNRNLTLTKKEPVGVCGIVIPWNYPLMMLSWKTAACLAAGNTVVIKPAQVTPLTALKFAELTLKAGIPKGVVNILPGSGSLVGQRLSDHPDVRKIGFTGSTEVGKHIMKSCALSNVKKVSLELGGKSPLIIFADCDLNKAVQMGMSSVFFNKGENSIAAGRLFVEESIHNQFVQKVVEEVEKMKIGNPLERDTNHGPQNHEAHLRKLVEYCQRGVKEGATLVCGGNQVPRPGFFFQPTVFTDVEDHMYIAKEESFGPIMIISRFADGDVDAVLSRANATEFGLASGVFTRDINKALYVSDKLQAGTVFINTYNKTDVAAPFGGFKQSGFGKDLGEAALNEYLRIKTVTFEY 902
                                   414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894        


Chain D from PDB  Type:PROTEIN  Length:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee..eeee....eee..eee.hhhh.eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhh...eee........eeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh..............hhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhh.eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh..eeee..............eeee.....hhhhh......eeeeeee....hhhhhhhhh........eee..hhhhhhhhhhhh...eeee...........ee.hhhhh..ee.hhhhhhh.eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4go0 D 405 VINYVEKAVNKLTLQMPYQLFIGGEFVDAEGSKTYNTINPTDGSVICQVSLAQVSDVDKAVAAAKEAFENGLWGKINARDRGRLLYRLADVMEQHQEELATIEALDAGAVYTLALKTHVGMSIQTFRYFAGWCDKIQGATIPINQARPNRNLTLTKKEPVGVCGIVIPWNYPLMMLSWKTAACLAAGNTVVIKPAQVTPLTALKFAELTLKAGIPKGVVNILPGSGSLVGQRLSDHPDVRKIGFTGSTEVGKHIMKSCALSNVKKVSLELGGKSPLIIFADCDLNKAVQMGMSSVFFNKGENSIAAGRLFVEESIHNQFVQKVVEEVEKMKIGNPLERDTNHGPQNHEAHLRKLVEYCQRGVKEGATLVCGGNQVPRPGFFFQPTVFTDVEDHMYIAKEESFGPIMIISRFADGDVDAVLSRANATEFGLASGVFTRDINKALYVSDKLQAGTVFINTYNKTDVAAPFGGFKQSGFGKDLGEAALNEYLRIKTVTFEY 902
                                   414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894
   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  (0, 0)

(no "SCOP Domain" information available for 4GO0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GO0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GO0)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

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  AL1L1_RAT | P28037
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        AL1L1_RAT | P28037: 1s3i 2o2p 2o2q 2o2r 3rhj 3rhl 3rhm 3rho 3rhp 3rhq 3rhr 4gnz 4go2

(-) Related Entries Specified in the PDB File

4gnz 4go2