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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF T-PROTEIN OF THE GLYCINE CLEAVAGE SYSTEM

Authors :   H. H. Lee, D. J. Kim, H. J. Ahn, J. Y. Ha, S. W. Suh

Date :   24 Aug 04 (Deposition) - 07 Sep 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A

Keywords :   Aminomethyltransferase, T-Protein, Dihydrolipoic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. H. Lee, D. J. Kim, H. J. Ahn, J. Y. Ha, S. W. Suh
Crystal Structure Of T-Protein Of The Glycine Cleavage System: Cofactor Binding, Insights Into H-Protein Recognition, And Molecular Basis For Understanding Nonketotic Hyperglycinemia
J. Biol. Chem. V. 279 50514 2004
PubMed-ID: 15355973 | Reference-DOI: 10.1074/JBC.M409672200
(for further references see the PDB file header)

Molecule 1 - AMINOMETHYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.1.2.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	GLYCINE CLEAVAGE SYSTEM T PROTEIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	RED	1	Ligand/Ion	DIHYDROLIPOIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:20 , LEU A:224 , ARG A:227 , ASP A:228 , HOH A:1014	BINDING SITE FOR RESIDUE RED A 900

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

Asymmetric/Biological Unit

No.	Residues
1	Lys A:353	-	Pro A:354

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

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

(no "Exon" information available for 1WOR)

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
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Chain A from PDB  Type:PROTEIN  Length:362
 aligned with GCST_THEMA | Q9WY54 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:362
                                    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       310       320       330       340       350       360  
           GCST_THEMA     1 MKRTPLFEKHVELGAKMVDFAGWEMPLYYTSIFEEVMAVRKSVGMFDVSHMGEFLVKGPEAVSFIDFLITNDFSSLPDGKAIYSVMCNENGGIIDDLVVYKVSPDEALMVVNAANIEKDFNWIKSHSKNFDVEVSNISDTTALIAFQGPKAQETLQELVEDGLEEIAYYSFRKSIVAGVETLVSRTGYTGEDGFELMLEAKNAPKVWDALMNLLRKIDGRPAGLGARDVCRLEATYLLYGQDMDENTNPFEVGLSWVVKLNKDFVGKEALLKAKEKVERKLVALELSGKRIARKGYEVLKNGERVGEITSGNFSPTLGKSIALALVSKSVKIGDQLGVVFPGGKLVEALVVKKPFYRGSVRR 362
               SCOP domains d1wora2 A:1-278 Glycine cleavage system T protein, GcvT                                                                                                                                                                                                                               d1wora1 A:279-362 Glycine cleavage system T protein, GcvT                            SCOP domains
               CATH domains 1worA01 A:1-49,A:137-234                         ---------------------------------------------------------------------------------------1worA01 A:1-49,A:137-234 Probable tRNA modification gtpase trme; domain 1                         -----------------------------------------1worA04 A:276-362 Aminomethyltransferase beta-barrel domains                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh..eeeee..eeeeee..hhhhhhhhhhhh.eeee....eeeeee..hhhhhhhhhh..........eeeeeeee.....eeeeeeeeeee..eeeeee...hhhhhhhhhhh.......eeee....eeeeeee..hhhhhhhhhh...........eeeeee..eeeeee........eeeeeee..hhhhhhhhhhhhhh....ee.hhhhhhhhhhhh.............hhhhhhhhhhh.......hhhhhhhhhhh..eeeeeeee..........eeee..eeeeeeeeeeee....eeeeeeeee.......eeeeee...eeeeeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wor A   1 MKRTPLFEKHVELGAKMVDFAGWEMPLYYTSIFEEVMAVRKSVGMFDVSHMGEFLVKGPEAVSFIDFLITNDFSSLPDGKAIYSVMCNENGGIIDDLVVYKVSPDEALMVVNAANIEKDFNWIKSHSKNFDVEVSNISDTTALIAFQGPKAQETLQELVEDGLEEIAYYSFRKSIVAGVETLVSRTGYTGEDGFELMLEAKNAPKVWDALMNLLRKIDGRPAGLGARDVCRLEATYLLYGQDMDENTNPFEVGLSWVVKLNKDFVGKEALLKAKEKVERKLVALELSGKRIARKGYEVLKNGERVGEITSGNFSPTLGKSIALALVSKSVKIGDQLGVVFPGGKLVEALVVKKPFYRGSVRR 362
                                    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       310       320       330       340       350       360

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 "Pfam Domain" information available for 1WOR)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (GCST_THEMA | Q9WY54)

molecular function
	GO:0004047	aminomethyltransferase activity	Catalysis of the reaction: (6S)-tetrahydrofolate + S-aminomethyldihydrolipoylprotein = (6R)-5,10-methylenetetrahydrofolate + NH3 + dihydrolipoylprotein.
	GO:0008483	transaminase activity	Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
	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.
biological process
	GO:0006546	glycine catabolic process	The chemical reactions and pathways resulting in the breakdown of glycine, aminoethanoic acid.
	GO:0019464	glycine decarboxylation via glycine cleavage system	The chemical reactions and pathways resulting in the breakdown of glycine by oxidative cleavage to carbon dioxide, ammonia, and a methylene group, mediated by enzymes of the glycine cleavage complex.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.

Asymmetric/Biological Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Lys A:353 - Pro A:354	[ RasMol ]

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	1wor
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	2.1.2.10
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UniProtKB/Swiss-Prot
	GCST_THEMA \| Q9WY54	:	1woo 1wop 1wos

1woo	THE SAME PROTEIN COMPLEXED WITH TETRAHYDROFOLATE
1wop	THE SAME PROTEIN COMPLEXED WITH FOLINIC ACID
1wos	THE SAME PROTEIN OF NATIVE FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

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