1T7L - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF COBALAMIN-INDEPENDENT METHIONINE SYNTHASE FROM T. MARITIMA

Authors :   R. Pejchal, M. L. Ludwig

Date :   10 May 04 (Deposition) - 01 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Tim Barrel, Homocysteine, Methyltetrahydrofolate, Zinc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Pejchal, M. L. Ludwig
Cobalamin-Independent Methionine Synthase (Mete): A Face-To-Face Double Barrel That Evolved By Gene Duplication
Plos Biol. V. 3 E31 2005
PubMed-ID: 15630480 | Reference-DOI: 10.1371/JOURNAL.PBIO.0030031
(for further references see the PDB file header)

Molecule 1 - 5-METHYLTETRAHYDROPTEROYLTRIGLUTAMATE-- HOMOCYSTEINE METHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-151-D-TOPO
	Expression System Strain	:	BL21 STAR (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	METE, TM1286
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	METHIONINE SYNTHASE, VITAMIN-B12 INDEPENDENT ISOZYME, COBALAMIN-INDEPENDENT METHIONINE SYNTHASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	MRY	2	Ligand/Ion	MESO-ERYTHRITOL
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	MRY	1	Ligand/Ion	MESO-ERYTHRITOL
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	MRY	1	Ligand/Ion	MESO-ERYTHRITOL
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:85 , TYR A:388 , ARG A:391 , GLU A:635 , LYS A:662 , HOH A:1145	BINDING SITE FOR RESIDUE SO4 A 1350
2	AC2	SOFTWARE	ARG B:85 , GLU B:387 , TYR B:388 , ARG B:391 , GLU B:635 , LYS B:662 , HOH B:1466	BINDING SITE FOR RESIDUE SO4 B 1351
3	AC3	SOFTWARE	LYS B:104 , PHE B:106 , LEU B:156 , CYS B:205 , ILE B:587 , HOH B:1392 , HOH B:1510 , HOH B:1590	BINDING SITE FOR RESIDUE MRY B 1352
4	AC4	SOFTWARE	LYS A:104 , PHE A:106 , LEU A:156 , CYS A:205 , ILE A:587 , HOH A:854 , HOH A:905 , HOH A:1257 , HOH A:1322	BINDING SITE FOR RESIDUE MRY A 1353

Asymmetric Unit

No.	Residues
1	A:620	-	A:704
2	B:620	-	B:704

(no "Cis Peptide Bond" information available for 1T7L)

(no "SAP(SNP)/Variant" information available for 1T7L)

(no "PROSITE Motif" information available for 1T7L)

(no "Exon" information available for 1T7L)

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
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Chain A from PDB  Type:PROTEIN  Length:734
 aligned with METE_THEMA | Q9X112 from UniProtKB/Swiss-Prot  Length:734

    Alignment length:734
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729    
           METE_THEMA     - -MKAYAFGFPKIGEKREFKKALEDFWKGKITEEQFEEEMNKLRMYMVENYRKNVDVIPSNELSYYDFVLDTAVMVGAVPERFGEYRGLSTYFDMARGGKALEMTKFFNTNYHYLVPEIETEEFYLLENKPLEDYLFFKSKGIETAPWVIGPFTFLYLSKRNGEWIRRPNQMEKLLESLVSVYKEVFEKLVENGCKEILVNEPAFVCDLEKAHWDLILNVYRELSEFPLTVFTYYDSVSDYEACVSLPVKRLHFDFVSNEENLKNLEKHGFPEDKKLVAGVINGRQPWKVDLRKVASLVEKLGASAISNSCPLFHLPVTLELENNLPGGLKEKLAFAKEKLEELKMLKDFLEGKTFDLPNVSFEDFAVDLQAVERVRNLPEDSFRREKEYTERDRIQRERLNLPLFPTTTIGSFPQTPEVRKMRSKYRKGEISKEEYEAFIKEQIKKAIELQEEIGLDVLVHGEFERTDMVEFFAEKLNGIATTQNGWVLSYGSRCYRPPIIYGTVTRPEPMTLKEITYAQSLTEKPVKGMLTGPVTIMSWSYYREDIPEREIAYQIALAINEEVKDLEEAGIKIVQIDEPAFREKAPIKKSKWPEYFEWAINAFNLAANARPETQIHAHMCYSDFNEIIEYIHQLEFDVISIEASRSKGEIISAFENFKGWIKQIGVGVWDIHSPAVPSINEMREIVERVLRVLPKELIWINPDCGLKTRNWDEVIPSLRNMVALAKEMREKFE 733
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1t7lA01 A:0-363,A:483-497  [code=3.20.20.210, no name defined]                                                                                                                                                                                                                                                                                                              1t7lA02 A:364-482,A:498-733  [code=3.20.20.210, no name defined]                                                       1t7lA01        1t7lA02 A:364-482,A:498-733  [code=3.20.20.210, no name defined]                                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee................hhhhhh......hhhhhhhhhhhhhhhhhhhhhh...ee......hhhhhhhhhh...........hhhhhhhhh......eeee......eeee............hhhhhhhhhhhh.....eeeeehhhhhhhh.........hhhhhh....hhhhhhhhhh..hhhhh...eeee.hhhhh..hhhhhhhhhhhhhh.....eeee.......hh.hhh......eeee....hhhhhhhhhhh......eeeeee...........hhhhhhhhhh..eeee..hhhhh.............hhhhh.hhhhhhhhhhhhhhhhh................hhhhhhhh............hhhhhh.hhh.hhh.................................hhhhhhhhhh..hhhhhhhhh............hhhhhhhh..eeee......eeee..eee...eeeeeee.....hhhhhhhhhhh.....eeeeehhhhhhhh.ee....hhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhh...hhhhhh.hhhhhhhhhhhhh......eeeee........hhhhhh.....eeeee.....hhhhhhhhh......eeeee..........hhhhhhhhhhhhh...hhh.eeee........hhhhhhhhhhhhhhhh.hhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t7l A   0 FTKAYAFGFPKIGEKREFKKALEDFWKGKITEEQFEEEMNKLRMYMVENYRKNVDVIPSNELSYYDFVLDTAVMVGAVPERFGEYRGLSTYFDMARGGKALEMTKFFNTNYHYLVPEIETEEFYLLENKPLEDYLFFKSKGIETAPWVIGPFTFLYLSKRNGEWIRRPNQMEKLLESLVSVYKEVFEKLVENGCKEILVNEPAFVCDLEKAHWDLILNVYRELSEFPLTVFTYYDSVSDYEACVSLPVKRLHFDFVSNEENLKNLEKHGFPEDKKLVAGVINGRQPWKVDLRKVASLVEKLGASAISNSCPLFHLPVTLELENNLPGGLKEKLAFAKEKLEELKMLKDFLEGKTFDLPNVSFEDFAVDLQAVERVRNLPEDSFRREKEYTERDRIQRERLNLPLFPTTTIGSFPQTPEVRKMRSKYRKGEISKEEYEAFIKEQIKKAIELQEEIGLDVLVHGEFERTDMVEFFAEKLNGIATTQNGWVLSYGSRCYRPPIIYGTVTRPEPMTLKEITYAQSLTEKPVKGMLTGPVTIMSWSYYREDIPEREIAYQIALAINEEVKDLEEAGIKIVQIDEPAFREKAPIKKSKWPEYFEWAINAFNLAANARPETQIHAHMCYSDFNEIIEYIHQLEFDVISIEASRSKGEIISAFENFKGWIKQIGVGVWDIHSPAVPSINEMREIVERVLRVLPKELIWINPDCGLKTRNWDEVIPSLRNMVALAKEMREKFE 733
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729

Chain B from PDB  Type:PROTEIN  Length:731
 aligned with METE_THEMA | Q9X112 from UniProtKB/Swiss-Prot  Length:734

    Alignment length:734
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727    
           METE_THEMA     - ---MKAYAFGFPKIGEKREFKKALEDFWKGKITEEQFEEEMNKLRMYMVENYRKNVDVIPSNELSYYDFVLDTAVMVGAVPERFGEYRGLSTYFDMARGGKALEMTKFFNTNYHYLVPEIETEEFYLLENKPLEDYLFFKSKGIETAPWVIGPFTFLYLSKRNGEWIRRPNQMEKLLESLVSVYKEVFEKLVENGCKEILVNEPAFVCDLEKAHWDLILNVYRELSEFPLTVFTYYDSVSDYEACVSLPVKRLHFDFVSNEENLKNLEKHGFPEDKKLVAGVINGRQPWKVDLRKVASLVEKLGASAISNSCPLFHLPVTLELENNLPGGLKEKLAFAKEKLEELKMLKDFLEGKTFDLPNVSFEDFAVDLQAVERVRNLPEDSFRREKEYTERDRIQRERLNLPLFPTTTIGSFPQTPEVRKMRSKYRKGEISKEEYEAFIKEQIKKAIELQEEIGLDVLVHGEFERTDMVEFFAEKLNGIATTQNGWVLSYGSRCYRPPIIYGTVTRPEPMTLKEITYAQSLTEKPVKGMLTGPVTIMSWSYYREDIPEREIAYQIALAINEEVKDLEEAGIKIVQIDEPAFREKAPIKKSKWPEYFEWAINAFNLAANARPETQIHAHMCYSDFNEIIEYIHQLEFDVISIEASRSKGEIISAFENFKGWIKQIGVGVWDIHSPAVPSINEMREIVERVLRVLPKELIWINPDCGLKTRNWDEVIPSLRNMVALAKEMREK 731
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1t7lB01 B:-2-363,B:483-497  [code=3.20.20.210, no name defined]                                                                                                                                                                                                                                                                                                               1t7lB02 B:364-482,B:498-731  [code=3.20.20.210, no name defined]                                                       1t7lB01        1t7lB02 B:364-482,B:498-731  [code=3.20.20.210, no name defined]                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....ee......hhhhhhhhhh...........hhhhhhhhhh.....eeee......eeee............hhhhhhhhhhhh.....eeeeehhhhhhhh.........hhhhhh....hhhhhhhhhh.hhhhhh...eeee.hhhhh..hhhhhhhhhhhhhhh....eeee.......hhhhhhh.....eeee.........hhhhhh......eeeeee........hhhhhhhhhhhhh...eee..hhhhh.............hhhhh.hhhhhhhhhhhhhhhhh.....---................................hh.hhh.hhh..................................hhhhhh.....hhhhhhhhh............hhhhhhhh..eeee......eeee..eee...eeeeeee........hhhhhhh.......eeeehhhhhhhh.ee....hhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhh...hhhhhh.hhhhhhhhhhhhh......eeeee........hhhhhh.....eeeee.....hhhhhhhhh......eeeee..........hhhhhh.hhhhhh...hhh.eeee........hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t7l B  -2 DPFTKAYAFGFPKIGEKREFKKALEDFWKGKITEEQFEEEMNKLRMYMVENYRKNVDVIPSNELSYYDFVLDTAVMVGAVPERFGEYRGLSTYFDMARGGKALEMTKFFNTNYHYLVPEIETEEFYLLENKPLEDYLFFKSKGIETAPWVIGPFTFLYLSKRNGEWIRRPNQMEKLLESLVSVYKEVFEKLVENGCKEILVNEPAFVCDLEKAHWDLILNVYRELSEFPLTVFTYYDSVSDYEACVSLPVKRLHFDFVSNEENLKNLEKHGFPEDKKLVAGVINGRQPWKVDLRKVASLVEKLGASAISNSCPLFHLPVTLELENNLPGGLKEKLAFAKEKLEELKMLKDFLEGKTFD---VSFEDFAVDLQAVERVRNLPEDSFRREKEYTERDRIQRERLNLPLFPTTTIGSFPQTPEVRKMRSKYRKGEISKEEYEAFIKEQIKKAIELQEEIGLDVLVHGEFERTDMVEFFAEKLNGIATTQNGWVLSYGSRCYRPPIIYGTVTRPEPMTLKEITYAQSLTEKPVKGMLTGPVTIMSWSYYREDIPEREIAYQIALAINEEVKDLEEAGIKIVQIDEPAFREKAPIKKSKWPEYFEWAINAFNLAANARPETQIHAHMCYSDFNEIIEYIHQLEFDVISIEASRSKGEIISAFENFKGWIKQIGVGVWDIHSPAVPSINEMREIVERVLRVLPKELIWINPDCGLKTRNWDEVIPSLRNMVALAKEMREK 731
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       | - |     367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727    
                                                                                                                                                                                                                                                                                                                                                                                               355 359

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 '\|'

(no "SCOP Domain" information available for 1T7L)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: [code=3.20.20.210, no name defined] (35)

Thermotoga maritima. Organism_taxid: 2336. (6)

1a	1t7lA02	A:364-482,A:498-733
1b	1t7lB02	B:364-482,B:498-731
1c	1t7lB01	B:-2-363,B:483-497
1d	1t7lA01	A:0-363,A:483-497

(no "Pfam Domain" information available for 1T7L)

Asymmetric Unit(hide GO term definitions)

Chain A,B (METE_THEMA | Q9X112)

molecular function
	GO:0003871	5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity	Catalysis of the reaction: 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-methionine + tetrahydropteroyltri-L-glutamate.
	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: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: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.
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.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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	1t7l
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(no "Related Entries Specified in the PDB File" available for 1T7L)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

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