2VGW - JenaLib

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Title :   CRYSTAL STRUCTURE OF E53QBSSHMT OBTAINED IN THE PRESENCE OF GLYCINE AND 5-FOMYL TETRAHYDROFOLATE

Authors :   V. Rajaram, B. S. Bhavani, P. Kaul, V. Prakash, N. Appaji Rao, H. S. Savithri, M. R. N. Murthy

Date :   15 Nov 07 (Deposition) - 04 Dec 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.86

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

Keywords :   Shmt, E53Q, Fthf, Transferase, Enzyme Memory, Pyridoxal Phosphate, One-Carbon Metabolism, Plp-Dependent Enzymes (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Rajaram, B. S. Bhavani, P. Kaul, V. Prakash, N. Appaji Rao, H. S. Savithri, M. R. N. Murthy
Structure Determination And Biochemical Studies On Bacillus Stearothermophilus E53Q Serine Hydroxymethyltransferase And Its Complexes Provide Insights On Function And Enzyme Memory
Febs J. V. 274 4148 2007
PubMed-ID: 17651438 | Reference-DOI: 10.1111/J.1742-4658.2007.05943.X

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.1.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PRSET C
	Fragment	:	RESIDUES 1-405
	Mutation	:	YES
	Organism Scientific	:	BACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 4)

No.	Name	Count	Type	Full Name
1	GLY	1	Mod. Amino Acid	GLYCINE
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (4, 8)

No.	Name	Count	Type	Full Name
1	GLY	2	Mod. Amino Acid	GLYCINE
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:51 , GLN A:53 , SER A:93 , GLY A:94 , ALA A:95 , HIS A:122 , ALA A:171 , SER A:172 , ASP A:197 , ALA A:199 , HIS A:200 , THR A:223 , HIS A:225 , LYS A:226 , GLY A:256 , GLY A:257 , GLY A:1408 , HOH A:2281 , HOH A:2282 , HOH A:2283 , HOH A:2284	BINDING SITE FOR RESIDUE PLP A1407
2	AC2	SOFTWARE	SER A:31 , TYR A:51 , TYR A:61 , SER A:172 , HIS A:200 , LYS A:226 , ARG A:357 , PLP A:1407	BINDING SITE FOR RESIDUE GLY A1408
3	AC3	SOFTWARE	TYR A:152 , ARG A:156 , GLU A:185 , LEU A:322 , HOH A:2285 , HOH A:2286 , HOH A:2287	BINDING SITE FOR RESIDUE MPD A1409
4	AC4	SOFTWARE	HOH A:2288	BINDING SITE FOR RESIDUE PO4 A1410

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

Asymmetric Unit

No.	Residues
1	Phe A:251	-	Pro A:252

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

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

(no "Exon" information available for 2VGW)

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:407
 aligned with Q7SIB6_GEOSE | Q7SIB6 from UniProtKB/TrEMBL  Length:419

    Alignment length:413
                                    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       370       380       390       400       410   
        Q7SIB6_GEOSE      1 MKYLPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNKYAEGYPGRRYYGGCEYVDIVEELARERAKQLFGAEHANVQPHSGAQANMAVYFTVLEHGDTVLGMNLSHGGHLTHGSPVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVAAASAYPRIIDFAKFREIADEVGAYLMVDMAHIAGLVAAGLHPNPVPYAHFVTTTTHKTLRGPRGGMILCQEQFAKQIDKAIFPGIQGGPLMHVIAAKAVAFGEALQDDFKAYAKRVVDNAKRLASALQNEGFTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITVNKNTIPYDPESPFVTSGIRIGTAAVTTRGFGLEEMDEIAAIIGLVLKNVGSEQALEEARQRVAALTDPTSRSAAG  413
               SCOP domains d2vgwa_ A: Serine hydroxymethyltransferase                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2vgwA01 A:1-32,A:284-406        2vgwA02 A:33-283 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                       2vgwA01 A:1-32,A:284-406 Aspartate Aminotransferase, domain 1                                                              ------- CATH domains
               Pfam domains ---SHMT-2vgwA01 A:4-380                                                                                                                                                                                                                                                                                                                                                                     --------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee.hhhh.hhhhh...hhhhhhheeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhh.eeeee...hhhhhhh...........eeeee.hhhhh....eeeee...hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.------. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2vgw A    1 MKYLPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNKYAQGYPGRRYYGGCEYVDIVEELARERAKQLFGAEHANVQPHSGAQANMAVYFTVLEHGDTVLGMNLSHGGHLTHGSPVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVAAASAYPRIIDFAKFREIADEVGAYLMVDMAHIAGLVAAGLHPNPVPYAHFVTTTTHKTLRGPRGGMILCQEQFAKQIDKAIFPGIQGGPLMHVIAAKAVAFGEALQDDFKAYAKRVVDNAKRLASALQNEGFTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITVNKNTIPYDPESPFVTSGIRIGTAAVTTRGFGLEEMDEIAAIIGLVLKNVGSEQALEEARQRVAALTDG------G 1408
                                    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       370       380       390       400     |   -  |
                                                                                                                                                                                                                                                                                                                                                                                                                                               406   1408

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: PLP-dependent transferase-like (627)

Superfamily: PLP-dependent transferases (625)

Family: GABA-aminotransferase-like (167)

Protein domain: Serine hydroxymethyltransferase (50)

Bacillus stearothermophilus [TaxId: 1422] (39)

d2vgwa_

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PLP_aminotran (240)

Family: SHMT (45)

Geobacillus stearothermophilus (Bacillus stearothermophilus) (38)

SHMT-2vgwA01

A:4-380

Asymmetric Unit(hide GO term definitions)

Chain A (Q7SIB6_GEOSE | Q7SIB6)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004372	glycine hydroxymethyltransferase activity	Catalysis of the reaction: 5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine.
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
	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:0006563	L-serine metabolic process	The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
	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:0006545	glycine biosynthetic process	The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
	GO:0019264	glycine biosynthetic process from serine	The chemical reactions and pathways resulting in the formation of glycine from other compounds, including serine.
	GO:0006544	glycine metabolic process	The chemical reactions and pathways involving glycine, aminoethanoic acid.
	GO:0006730	one-carbon metabolic process	The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
	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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		GLY	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MPD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PLP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Phe A:251 - Pro A:252	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2vgw
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	2.1.2.1
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1kkj	CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE FROMB.STEAROTHERMOPHILUS
1kkp	CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASECOMPLEXED WITH SERINE
1kl1	CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASECOMPLEXED WITH GLYCINE
1kl2	CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASECOMPLEXED WITH GLYCINE AND 5-FORMYL TETRAHYDROFOLATE
1yjs	K226Q MUTANT OF SERINE HYDROXYMETHYLTRANSFERASE FROM B.STEAROTHERMOPHILUS, COMPLEX WITH GLYCINE
1yjy	K226M MUTANT OF SERINE HYDROXYMETHYLTRANSFERASE FROM B.STEAROTHERMOPHILUS, COMPLEX WITH SERINE
1yjz	K226M MUTANT OF SERINE HYDROXYMETHYLTRANSFERASE FROM B.STEAROTHERMOPHILUS
2vgs	CRYSTAL STRUCTURE OF E53QBSSHMT INTERNAL ALDIMINE
2vgt	CRYSTAL STRUCTURE OF E53QBSSHMT WITH GLYCINE
2vgu	CRYSTAL STRUCTURE OF E53QBSSHMT WITH L- SERINE
2vgv	CRYSTAL STRUCTURE OF E53QBSSHMT OBTAINED IN THE PRESENCE OF L-ALLO-THREONINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (2, 2)

Pfam Domains (1, 1)

Gene Ontology (12, 12)

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