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Title :   CRYSTAL STRUCTURE OF ESCHERICHIA COLI METHYLENETETRAHYDROFOLATE REDUCTASE MUTANT PHE223LEU AT PH 7.4

Authors :   J. J. Tanner

Date :   12 Jan 09 (Deposition) - 25 Aug 09 (Release) - 25 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym. Unit : A,C,E
Biol. Unit 1: A (2x),C (1x),E (1x)

Keywords :   Tim Barrel, Flavin, Reductase, Amino-Acid Biosynthesis, Fad, Flavoprotein, Methionine Biosynthesis, Nad, Nadp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. N. Lee, D. Takawira, A. P. Nikolova, D. P. Ballou, V. C. Furtado, N. L. Phung, B. R. Still, M. K. Thorstad, J. J. Tanner, E. E. Trimmer
Functional Role For The Conformationally Mobile Phenylalanine 223 In The Reaction Of Methylenetetrahydrofolate Reductase From Escherichia Coli.
Biochemistry V. 48 7673 2009
PubMed-ID: 19610625 | Reference-DOI: 10.1021/BI9007325
(for further references see the PDB file header)

Molecule 1 - 5,10-METHYLENETETRAHYDROFOLATE REDUCTASE
	Chains	:	A, C, E
	EC Number	:	1.5.1.20
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDTL2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	METF, B3941, JW3913
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI K-12
	Organism Taxid	:	83333

		1	2	3
Asymmetric Unit	:	A	C	E
Biological Unit 1 (2x)	:	A (2x)	C (1x)	E (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	FAD	3	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	MRY	1	Ligand/Ion	MESO-ERYTHRITOL
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	FAD	-1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	MRY	-1	Ligand/Ion	MESO-ERYTHRITOL
3	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:59 , TYR A:60 , ALA A:62 , HIS A:88 , LEU A:117 , ARG A:118 , GLY A:119 , ASP A:120 , TYR A:131 , ALA A:132 , ALA A:150 , TYR A:152 , HIS A:156 , GLU A:158 , ALA A:159 , ASP A:165 , ASN A:168 , ARG A:171 , LYS A:172 , ILE A:181 , GLN A:183 , TYR A:275 , HOH A:322 , HOH A:336 , HOH A:363 , HOH A:367 , HOH A:402 , HOH A:438	BINDING SITE FOR RESIDUE FAD A 395
2	AC2	SOFTWARE	THR C:59 , TYR C:60 , HIS C:88 , LEU C:117 , ARG C:118 , GLY C:119 , ASP C:120 , TYR C:131 , ALA C:132 , ALA C:150 , TYR C:152 , HIS C:156 , GLU C:158 , ALA C:159 , ASP C:165 , ASN C:168 , ARG C:171 , LYS C:172 , ILE C:181 , GLN C:183 , TYR C:275 , HOH C:340 , HOH C:343 , HOH C:375 , HOH C:393 , HOH C:450 , HOH C:488 , HOH C:491 , HOH C:517 , MRY C:5321	BINDING SITE FOR RESIDUE FAD C 396
3	AC3	SOFTWARE	THR E:59 , TYR E:60 , HIS E:88 , THR E:90 , LEU E:117 , ARG E:118 , GLY E:119 , ASP E:120 , TYR E:131 , ALA E:132 , ALA E:150 , TYR E:152 , HIS E:156 , ALA E:159 , ASP E:165 , ASN E:168 , ARG E:171 , LYS E:172 , ILE E:181 , GLN E:183 , TYR E:275 , HOH E:315 , HOH E:447	BINDING SITE FOR RESIDUE FAD E 397
4	AC4	SOFTWARE	GLU C:28 , GLN C:183 , PHE C:184 , TYR C:275 , LEU C:277 , HOH C:360 , HOH C:394 , FAD C:396 , HOH C:459	BINDING SITE FOR RESIDUE MRY C 5321
5	AC5	SOFTWARE	ARG E:230 , PRO E:232 , ALA E:233 , TRP E:234 , HOH E:465	BINDING SITE FOR RESIDUE SO4 E 305
6	AC6	SOFTWARE	ARG A:279 , ALA A:280 , GLU A:281 , HOH A:318 , HOH A:426 , HOH E:520	BINDING SITE FOR RESIDUE SO4 E 306
7	AC7	SOFTWARE	SER E:44 , ARG E:279 , ALA E:280 , GLU E:281 , HOH E:329 , HOH E:521	BINDING SITE FOR RESIDUE SO4 E 307

(no "SS Bond" information available for 3FST)

(no "Cis Peptide Bond" information available for 3FST)

(no "SAP(SNP)/Variant" information available for 3FST)

(no "PROSITE Motif" information available for 3FST)

(no "Exon" information available for 3FST)

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:286
 aligned with METF_ECOLI | P0AEZ1 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:292
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292  
           METF_ECOLI     3 FFHASQRDALNQSLAEVQGQINVSFEFFPPRTSEMEQTLWNSIDRLSSLKPKFVSVTYGANSGERDRTHSIIKGIKDRTGLEAAPHLTCIDATPDELRTIARDYWNNGIRHIVALRGDLPPGSGKPEMYASDLVTLLKEVADFDISVAAYPEVHPEAKSAQADLLNLKRKVDAGANRAITQFFFDVESYLRFRDRCVSAGIDVEIIPGILPVSNFKQAKKFADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMVKILSREGVKDFHFYTLNRAEMSYAICHTLGVRP 294
               SCOP domains d3fsta_ A: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3fstA00 A:3-294  [code=3.20.20.220, no name defined]                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhh...eeeee.....------..hhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh.....ee.ee....hhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fst A   3 FFHASQRDALNQSLAEVQGQINVSFEFFPPRTSEMEQTLWNSIDRLSSLKPKFVSVTYGANSGERDRTHSIIKGIKDRTGLEAAPHLTCIDATPDELRTIARDYWNNGIRHIVALRGDLP------EMYASDLVTLLKEVADFDISVAAYPEVHPEAKSAQADLLNLKRKVDAGANRAITQFFFDVESYLRFRDRCVSAGIDVEIIPGILPVSNFKQAKKLADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMVKILSREGVKDFHFYTLNRAEMSYAICHTLGVRP 294
                                    12        22        32        42        52        62        72        82        92       102       112       122      |132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292  
                                                                                                                                                 122    129

Chain C from PDB  Type:PROTEIN  Length:265
 aligned with METF_ECOLI | P0AEZ1 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:273
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
           METF_ECOLI    22 QINVSFEFFPPRTSEMEQTLWNSIDRLSSLKPKFVSVTYGANSGERDRTHSIIKGIKDRTGLEAAPHLTCIDATPDELRTIARDYWNNGIRHIVALRGDLPPGSGKPEMYASDLVTLLKEVADFDISVAAYPEVHPEAKSAQADLLNLKRKVDAGANRAITQFFFDVESYLRFRDRCVSAGIDVEIIPGILPVSNFKQAKKFADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMVKILSREGVKDFHFYTLNRAEMSYAICHTLGVRP 294
               SCOP domains d3fstc_ C: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3fstC00 C:22-294  [code=3.20.20.220, no name defined]                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhh...eeeee...--------..hhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh....eee.ee....hhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fst C  22 QINVSFEFFPPRTSEMEQTLWNSIDRLSSLKPKFVSVTYGANSGERDRTHSIIKGIKDRTGLEAAPHLTCIDATPDELRTIARDYWNNGIRHIVALRGD--------EMYASDLVTLLKEVADFDISVAAYPEVHPEAKSAQADLLNLKRKVDAGANRAITQFFFDVESYLRFRDRCVSAGIDVEIIPGILPVSNFKQAKKLADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMVKILSREGVKDFHFYTLNRAEMSYAICHTLGVRP 294
                                    31        41        51        61        71        81        91       101       111        |-       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
                                                                                                                            120      129

Chain E from PDB  Type:PROTEIN  Length:274
 aligned with METF_ECOLI | P0AEZ1 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:291
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293 
           METF_ECOLI     4 FHASQRDALNQSLAEVQGQINVSFEFFPPRTSEMEQTLWNSIDRLSSLKPKFVSVTYGANSGERDRTHSIIKGIKDRTGLEAAPHLTCIDATPDELRTIARDYWNNGIRHIVALRGDLPPGSGKPEMYASDLVTLLKEVADFDISVAAYPEVHPEAKSAQADLLNLKRKVDAGANRAITQFFFDVESYLRFRDRCVSAGIDVEIIPGILPVSNFKQAKKFADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMVKILSREGVKDFHFYTLNRAEMSYAICHTLGVRP 294
               SCOP domains d3fste_ E: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3fstE00 E:4-294  [code=3.20.20.220, no name defined]                                                                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhh....eeee..---------hhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhh....eeeee...--------..hhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh.....ee.ee....hhhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fst E   4 FHASQRDALNQSLAEVQGQINVSFEFFPPRTSEMEQTLWNSIDRLSSLKPKFVSVTY---------THSIIKGIKDRTGLEAAPHLTCIDATPDELRTIARDYWNNGIRHIVALRGD--------EMYASDLVTLLKEVADFDISVAAYPEVHPEAKSAQADLLNLKRKVDAGANRAITQFFFDVESYLRFRDRCVSAGIDVEIIPGILPVSNFKQAKKLADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMVKILSREGVKDFHFYTLNRAEMSYAICHTLGVRP 294
                                    13        23        33        43        53      |  -      | 73        83        93       103       113      |  -     | 133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293 
                                                                                   60        70                                               120      129

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: FAD-linked oxidoreductase (25)

Family: Methylenetetrahydrofolate reductase (12)

Protein domain: automated matches (4)

Escherichia coli K-12 [TaxId: 83333] (2)

1a	d3fsta_	A:
1b	d3fstc_	C:
1c	d3fste_	E:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: [code=3.20.20.220, no name defined] (15)

Escherichia coli k-12. Organism_taxid: 83333. (2)

1a	3fstA00	A:3-294
1b	3fstE00	E:4-294
1c	3fstC00	C:22-294

(no "Pfam Domain" information available for 3FST)

Asymmetric Unit(hide GO term definitions)

Chain A,C,E (METF_ECOLI | P0AEZ1)

molecular function
	GO:0071949	FAD binding	Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0004489	methylenetetrahydrofolate reductase (NAD(P)H) activity	Catalysis of the reaction: 5-methyltetrahydrofolate + NAD(P)+ = 5,10-methylenetetrahydrofolate + NAD(P)H + 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:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0009086	methionine biosynthetic process	The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
	GO:0006555	methionine metabolic process	The chemical reactions and pathways involving methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
	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:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
	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.
	GO:0035999	tetrahydrofolate interconversion	The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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