2FMN - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   ALA177VAL MUTANT OF E. COLI METHYLENETETRAHYDROFOLATE REDUCTASE COMPLEX WITH LY309887

Authors :   R. Pejchal, E. Campbell, B. D. Guenther, B. W. Lennon, R. G. Matthews, M. L. Ludwig

Date :   09 Jan 06 (Deposition) - 25 Apr 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

Keywords :   Oxidoreductase, Tim Barrel, Flavin, Reductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Pejchal, E. Campbell, B. D. Guenther, B. W. Lennon, R. G. Matthews, M. L. Ludwig
Structural Perturbations In The Ala -> Val Polymorphism Of Methylenetetrahydrofolate Reductase: How Binding Of Folates May Protect Against Inactivation
Biochemistry V. 45 4808 2006
PubMed-ID: 16605249 | Reference-DOI: 10.1021/BI052294C
(for further references see the PDB file header)

Molecule 1 - 5,10-METHYLENETETRAHYDROFOLATE REDUCTASE
	Chains	:	A, B, C
	EC Number	:	1.5.1.20
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET23B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	METF
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	4HF	3	Ligand/Ion	N-[(5-{2-[(6R)-2-AMINO-4-OXO-3,4,5,6,7,8-HEXAHYDROPYRIDO[2,3-D]PYRIMIDIN-6-YL]ETHYL}-2-THIENYL)CARBONYL]-L-GLUTAMIC ACID
2	FAD	3	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	4HF	-1	Ligand/Ion	N-[(5-{2-[(6R)-2-AMINO-4-OXO-3,4,5,6,7,8-HEXAHYDROPYRIDO[2,3-D]PYRIMIDIN-6-YL]ETHYL}-2-THIENYL)CARBONYL]-L-GLUTAMIC ACID
2	FAD	-1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:59 , TYR A:60 , HIS A:88 , THR A:90 , 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 , LYS A:172 , ILE A:181 , GLN A:183 , TYR A:275 , 4HF A:495 , HOH A:594 , HOH A:595 , HOH A:596 , HOH A:698 , HOH A:733 , HOH A:736	BINDING SITE FOR RESIDUE FAD A 395
2	AC2	SOFTWARE	GLU A:28 , PHE A:30 , ASP A:120 , GLN A:183 , PHE A:184 , GLN A:219 , PHE A:223 , THR A:227 , TYR A:275 , LEU A:277 , FAD A:395 , HOH A:629 , HOH A:738	BINDING SITE FOR RESIDUE 4HF A 495
3	AC3	SOFTWARE	THR B:59 , TYR B:60 , HIS B:88 , LEU B:117 , ARG B:118 , GLY B:119 , ASP B:120 , TYR B:131 , ALA B:132 , ALA B:150 , TYR B:152 , HIS B:156 , GLU B:158 , ALA B:159 , ASP B:165 , ASN B:168 , LYS B:172 , ILE B:181 , GLN B:183 , TYR B:275 , 4HF B:496 , HOH B:512 , HOH B:516 , HOH B:528 , HOH B:536 , HOH B:612	BINDING SITE FOR RESIDUE FAD B 396
4	AC4	SOFTWARE	GLU B:28 , PHE B:30 , ARG B:33 , ASP B:120 , GLN B:183 , PHE B:184 , LEU B:212 , GLN B:219 , PHE B:223 , THR B:227 , TYR B:275 , LEU B:277 , FAD B:396 , HOH B:658 , HOH B:755	BINDING SITE FOR RESIDUE 4HF B 496
5	AC5	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 , LYS C:172 , ILE C:181 , GLN C:183 , TYR C:275 , 4HF C:497 , HOH C:509 , HOH C:514 , HOH C:543 , HOH C:603 , HOH C:709	BINDING SITE FOR RESIDUE FAD C 397
6	AC6	SOFTWARE	GLU C:28 , PHE C:30 , ASP C:120 , GLN C:183 , GLN C:219 , PHE C:223 , TYR C:275 , LEU C:277 , FAD C:397 , HOH C:756	BINDING SITE FOR RESIDUE 4HF C 497

(no "SS Bond" information available for 2FMN)

(no "Cis Peptide Bond" information available for 2FMN)

(no "SAP(SNP)/Variant" information available for 2FMN)

(no "PROSITE Motif" information available for 2FMN)

(no "Exon" information available for 2FMN)

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:288
 aligned with METF_ECOLI | P0AEZ1 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:293
                                    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 FFHASQRDALNQSLAEVQGQINVSFEFFPPRTSEMEQTLWNSIDRLSSLKPKFVSVTYGANSGERDRTHSIIKGIKDRTGLEAAPHLTCIDATPDELRTIARDYWNNGIRHIVALRGDLPPGSGKPEMYASDLVTLLKEVADFDISVAAYPEVHPEAKSAQADLLNLKRKVDAGANRAITQFFFDVESYLRFRDRCVSAGIDVEIIPGILPVSNFKQAKKFADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMVKILSREGVKDFHFYTLNRAEMSYAICHTLGVRPG 295
               SCOP domains d2fmna_ A: Methylenetetrahydrofolate reductase                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2fmnA00 A:3-295  [code=3.20.20.220, no name defined]                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh....eeee.......-----..hhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh.....ee.ee....hhhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fmn A   3 FFHASQRDALNQSLAEVQGQINVSFEFFPPRTSEMEQTLWNSIDRLSSLKPKFVSVTYGANSGERDRTHSIIKGIKDRTGLEAAPHLTCIDATPDELRTIARDYWNNGIRHIVALRGDLPP-----EMYASDLVTLLKEVADFDISVAAYPEVHPEAKSAQADLLNLKRKVDAGVNRAITQFFFDVESYLRFRDRCVSAGIDVEIIPGILPVSNFKQAKKFADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMVKILSREGVKDFHFYTLNRAEMSYAICHTLGVRPG 295
                                    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   
                                                                                                                                                  123   129

Chain B from PDB  Type:PROTEIN  Length:287
 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 d2fmnb_ B: Methylenetetrahydrofolate reductase                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2fmnB00 B:3-294  [code=3.20.20.220, no name defined]                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh...eeee.......-----..hhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh.....ee.ee....hhhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fmn B   3 FFHASQRDALNQSLAEVQGQINVSFEFFPPRTSEMEQTLWNSIDRLSSLKPKFVSVTYGANSGERDRTHSIIKGIKDRTGLEAAPHLTCIDATPDELRTIARDYWNNGIRHIVALRGDLPP-----EMYASDLVTLLKEVADFDISVAAYPEVHPEAKSAQADLLNLKRKVDAGVNRAITQFFFDVESYLRFRDRCVSAGIDVEIIPGILPVSNFKQAKKFADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMVKILSREGVKDFHFYTLNRAEMSYAICHTLGVRP 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  
                                                                                                                                                  123   129

Chain C from PDB  Type:PROTEIN  Length:271
 aligned with METF_ECOLI | P0AEZ1 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:276
                                    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      
           METF_ECOLI    21 GQINVSFEFFPPRTSEMEQTLWNSIDRLSSLKPKFVSVTYGANSGERDRTHSIIKGIKDRTGLEAAPHLTCIDATPDELRTIARDYWNNGIRHIVALRGDLPPGSGKPEMYASDLVTLLKEVADFDISVAAYPEVHPEAKSAQADLLNLKRKVDAGANRAITQFFFDVESYLRFRDRCVSAGIDVEIIPGILPVSNFKQAKKFADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMVKILSREGVKDFHFYTLNRAEMSYAICHTLGVRPGL 296
               SCOP domains d2fmnc_ C: Methylenetetrahydrofolate reductase                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2fmnC00 C:21-296  [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
                 2fmn C  21 GQINVSFEFFPPRTSEMEQTLWNSIDRLSSLKPKFVSVTYGANSGERDRTHSIIKGIKDRTGLEAAPHLTCIDATPDELRTIARDYWNNGIRHIVALRGDLP-----PEMYASDLVTLLKEVADFDISVAAYPEVHPEAKSAQADLLNLKRKVDAGVNRAITQFFFDVESYLRFRDRCVSAGIDVEIIPGILPVSNFKQAKKFADMTNVRIPAWMAQMFDGLDDDAETRKLVGANIAMDMVKILSREGVKDFHFYTLNRAEMSYAICHTLGVRPGL 296
                                    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      
                                                                                                                               122   128

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

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: Methylenetetrahydrofolate reductase (8)

Escherichia coli [TaxId: 562] (7)

1a	d2fmna_	A:
1b	d2fmnb_	B:
1c	d2fmnc_	C:

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. Organism_taxid: 562. (11)

1a	2fmnA00	A:3-295
1b	2fmnB00	B:3-294
1c	2fmnC00	C:21-296

(no "Pfam Domain" information available for 2FMN)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (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.

Asymmetric Unit
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Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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