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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HYDROLASE DOMAIN OF 10-FORMYLTETRAHYDROFOLATE DEHYDROGENASE (WILD-TYPE) COMPLEX WITH TETRAHYDROFOLATE
 
Authors :  C. C. Lin, C. J. Chen, T. F. Fu, P. Chuankhayan, T. T. Kao, W. N. Chang
Date :  23 Jun 14  (Deposition) - 15 Apr 15  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  10-Formyltetrahydrofolate Dehydrogenase, Hydrolase Domain, Catalysis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. C. Lin, P. Chuankhayan, W. N. Chang, T. T. Kao, H. H. Guan, H. K. Fun, A. Nakagawa, T. F. Fu, C. J. Chen
Structures Of The Hydrolase Domain Of Zebrafish 10-Formyltetrahydrofolate Dehydrogenase And Its Complexes Reveal A Complete Set Of Key Residues For Hydrolysis And Product Inhibition
Acta Crystallogr. , Sect. D V. 71 1006 2015
PubMed: search  |  Reference-DOI: 10.1107/S1399004715002928

(-) Compounds

Molecule 1 - 10-FORMYLTETRAHYDROFOLATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.5.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-311
    Gene: ALDH1L1
    Organism Common: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955

 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, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
2THG3Ligand/Ion(6S)-5,6,7,8-TETRAHYDROFOLATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
2THG1Ligand/Ion(6S)-5,6,7,8-TETRAHYDROFOLATE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
2THG2Ligand/Ion(6S)-5,6,7,8-TETRAHYDROFOLATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:85 , TYR A:164BINDING SITE FOR RESIDUE PEG A 401
2AC2SOFTWARECYS A:86 , GLN A:88 , PHE A:89 , ILE A:90 , ILE A:95 , ILE A:104 , GLY A:115 , ALA A:116 , ASP A:138 , GLY A:140 , LEU A:141 , ASP A:142 , TYR A:200 , LYS A:205 , HOH A:502 , HOH A:599 , HOH A:630 , ASN B:283 , HOH B:646 , HOH B:689BINDING SITE FOR RESIDUE THG A 402
3AC3SOFTWAREPHE B:85 , TYR B:164 , HOH B:638BINDING SITE FOR RESIDUE PEG B 401
4AC4SOFTWAREARG A:114 , TYR A:200 , SER B:257 , ASN B:258 , GLY B:259 , SER B:268 , ARG B:269 , LEU B:272 , PHE B:281 , GLY B:282 , GLY B:285 , HOH B:653 , HOH B:654BINDING SITE FOR RESIDUE THG B 402
5AC5SOFTWARECYS B:86 , SER B:87 , GLN B:88 , PHE B:89 , ILE B:90 , ILE B:95 , ILE B:104 , ASP B:138 , GLY B:140 , LEU B:141 , ASP B:142 , TYR B:200 , ILE B:203 , HOH B:619 , HOH B:625 , HOH B:659 , HOH B:668 , HOH B:669 , HOH B:673 , HOH B:690BINDING SITE FOR RESIDUE THG B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Leu A:110 -Pro A:111
2Asp A:228 -Arg A:229
3Val A:230 -Pro A:231
4Asn A:252 -Asp A:253
5His A:254 -Phe A:255
6Phe A:255 -Ser A:256
7Leu B:110 -Pro B:111
8Asp B:228 -Arg B:229
9Val B:230 -Pro B:231
10Asn B:252 -Asp B:253
11His B:254 -Phe B:255
12Ser B:256 -Ser B:257

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QPD)

(-) 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:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhh..ee...........hhhhhhhhhh....eeee.......hhhhhh.....eeeee..........hhhhhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..............................hhhhhhhhhhh......eeeee..eeeeeeeeeee.........eee........eeee..eeeee.....eeeeeeeee.....ee.hhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qpd A   1 MKIAVIGQSLFGQEVYKELKNEGHMIVGVFTIPDKDGKVDPLAIEAEKDGVPVFKFPRWRLKGKAITEVVDQYKAVGAELNVLPFCSQFIPMEVIDHPKHGSIIYHPSLLPRHRGASAINWTLIHGDKKGGFTVFWADDGLDTGPILLQRECDVEPNDNVNSIYKRFLFPEGVKGMVEAVRLIATGKAPRIKQPEEGATYECIQKKENSKIDWNQPAEAIHNWIRGNDRVPGAWAEIDGKSVSFYGSTLLENDHFSSNGQPLEIPGASRAALVTKNGLVLFGNDGKMLLVKNLQFEDGKMIPGSQYFK 308
                                    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        


Chain B from PDB  Type:PROTEIN  Length:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhh...ee.....ee..eehhhhhhhhhh....eeee.......hhhhhh.....eeeee..........hhhhhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhh.....hhhhhhhhhhh.......eeee..eeeeeeeeeee.........eee........eeee..eeeee.....eeeeeeee.hhh.eee.hhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qpd B   1 MKIAVIGQSLFGQEVYKELKNEGHMIVGVFTIPDKDGKVDPLAIEAEKDGVPVFKFPRWRLKGKAITEVVDQYKAVGAELNVLPFCSQFIPMEVIDHPKHGSIIYHPSLLPRHRGASAINWTLIHGDKKGGFTVFWADDGLDTGPILLQRECDVEPNDNVNSIYKRFLFPEGVKGMVEAVRLIATGKAPRIKQPEEGATYECIQKKENSKIDWNQPAEAIHNWIRGNDRVPGAWAEIDGKSVSFYGSTLLENDHFSSNGQPLEIPGASRAALVTKNGLVLFGNDGKMLLVKNLQFEDGKMIPGSQYFK 308
                                    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
   Legend:   → Mismatch (orange background)
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  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 4QPD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        E3NZ06_DANRE | E3NZ06: 4qpc 4r8v 4ts4 4tt8 4tts

(-) Related Entries Specified in the PDB File

4qpc THE SAME PROTEIN IN MUTANT TYPE (Y200A)
4r8v
4ts4 THE SAME PROTEIN IN WILD TYPE
4tt8 THE SAME PROTEIN (WILD TYPE) AND COMPLEX WITH 10-FORMYL-5, 8-DIDEAZAFOLATE
4tts THE SAME PROTEIN (Y200A) AND COMPLEX WITH 10-FORMYL-5,8- DIDEAZAFOLATE