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Title :   HOW A PROTEIN BINDS B12: A 3.O ANGSTROM X-RAY STRUCTURE OF THE B12-BINDING DOMAINS OF METHIONINE SYNTHASE

Authors :   C. L. Drennan, S. Huang, J. T. Drummond, R. G. Matthews, M. L. Ludwig

Date :   02 Sep 94 (Deposition) - 03 Jun 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Methyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. L. Drennan, S. Huang, J. T. Drummond, R. G. Matthews, M. L. Lidwig
How A Protein Binds B12: A 3. 0 A X-Ray Structure Of B12-Binding Domains Of Methionine Synthase.
Science V. 266 1669 1994
PubMed-ID: 7992050
(for further references see the PDB file header)

Molecule 1 - METHIONINE SYNTHASE
	Chains	:	A, B
	EC Number	:	2.1.1.13
	Engineered	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	COB	2	Ligand/Ion	CO-METHYLCOBALAMIN

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:694 , MET A:698 , MET A:701 , GLY A:705 , LEU A:715 , VAL A:718 , GLY A:756 , ASP A:757 , VAL A:758 , HIS A:759 , ASP A:760 , ILE A:761 , GLY A:762 , ILE A:765 , GLY A:802 , LEU A:803 , SER A:804 , LEU A:806 , ILE A:807 , THR A:808 , LEU A:831 , GLY A:834 , ALA A:835 , VAL A:857 , GLN A:858 , ASN A:859 , ALA A:860 , THR A:863 , GLN B:677 , GLU B:680 , ARG B:683 , TYR B:731 , PHE B:735	BINDING SITE FOR RESIDUE COB A 122
2	AC2	SOFTWARE	ALA A:738 , GLU A:741 , GLU B:694 , MET B:698 , MET B:701 , VAL B:704 , GLY B:705 , LEU B:715 , VAL B:718 , MET B:725 , ILE B:751 , GLY B:756 , ASP B:757 , VAL B:758 , HIS B:759 , ASP B:760 , ILE B:761 , GLY B:762 , ILE B:765 , GLY B:802 , LEU B:803 , SER B:804 , LEU B:806 , ILE B:807 , THR B:808 , GLY B:834 , ALA B:835 , GLN B:858 , ASN B:859 , ALA B:860 , THR B:863	BINDING SITE FOR RESIDUE COB B 122

(no "SS Bond" information available for 1BMT)

(no "Cis Peptide Bond" information available for 1BMT)

(no "SAP(SNP)/Variant" information available for 1BMT)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	B12_BINDING	PS51332	B12-binding domain profile.	METH_ECOLI	746-881	2	A:746-881 B:746-881

(no "Exon" information available for 1BMT)

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:246
 aligned with METH_ECOLI | P13009 from UniProtKB/Swiss-Prot  Length:1227

    Alignment length:246
                                   660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890      
           METH_ECOLI   651 QAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGR 896
               SCOP domains d1bmta1 A:651-740 Methionine synthase domain                                              d1bmta2 A:741-896 Methionine synthase, C-terminal domain                                                                                                     SCOP domains
               CATH domains 1bmtA01 A:651-737 Methyltransferase                                                    1bmtA02 A:738-895  [code=3.40.50.280, no name defined]                                                                                                        - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhh..hhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee......hhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhh....eeeee....hhhhhhh..hhh...eeeee..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------B12_BINDING  PDB: A:746-881 UniProt: 746-881                                                                                            --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1bmt A 651 QAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGR 896
                                   660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890

Chain B from PDB  Type:PROTEIN  Length:246
 aligned with METH_ECOLI | P13009 from UniProtKB/Swiss-Prot  Length:1227

    Alignment length:246
                                   660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890      
           METH_ECOLI   651 QAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGR 896
               SCOP domains d1bmtb1 B:651-740 Methionine synthase domain                                              d1bmtb2 B:741-896 Methionine synthase, C-terminal domain                                                                                                     SCOP domains
               CATH domains 1bmtB01 B:651-737 Methyltransferase                                                    1bmtB02 B:738-895  [code=3.40.50.280, no name defined]                                                                                                        - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhh..hhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee......hhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhh....eeeee....hhhhhhh..hhh...eeeee..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------B12_BINDING  PDB: B:746-881 UniProt: 746-881                                                                                            --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1bmt B 651 QAEWRSWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGR 896
                                   660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.280, no name defined] (23)

Escherichia coli. Organism_taxid: 562 (1)

1a	1bmtA02	A:738-895
1b	1bmtB02	B:738-895

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 (21)

Homologous Superfamily: Methyltransferase (6)

Escherichia coli. Organism_taxid: 562 (1)

2a	1bmtA01	A:651-737
2b	1bmtB01	B:651-737

(no "Pfam Domain" information available for 1BMT)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (METH_ECOLI | P13009)

molecular function
	GO:0008898	S-adenosylmethionine-homocysteine S-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + L-homocysteine = S-adenosyl-L-homocysteine + L-methionine.
	GO:0031419	cobalamin binding	Interacting selectively and non-covalently with cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008705	methionine synthase activity	Catalysis of the reaction: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine = (6S)-5,6,7,8-tetrahydrofolate + L-methionine.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0008276	protein methyltransferase activity	Catalysis of the transfer of a methyl group (CH3-) to a protein.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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:0044237	cellular metabolic process	The chemical reactions and pathways by which individual cells transform chemical substances.
	GO:0050667	homocysteine metabolic process	The chemical reactions and pathways involving homocysteine, the amino acid alpha-amino-gamma-mercaptobutanoic acid. Homocysteine is an important intermediate in the metabolic reactions of its S-methyl derivative, methionine.
	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:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0006479	protein methylation	The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
	GO:0042558	pteridine-containing compound metabolic process	The chemical reactions and pathways involving any compound containing pteridine (pyrazino(2,3-dipyrimidine)), e.g. pteroic acid, xanthopterin and folic acid.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric/Biological Unit
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