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Title :   CRYSTAL STRUCTURE OF T.TH.HB8 SERINE HYDROXYMETHYLTRANSFERASE

Authors :   K. Kai, M. Goto, I. Miyahara, K. Hirotsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   11 Apr 06 (Deposition) - 24 Apr 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.15

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

Keywords :   Plp Dependent Enzyme, Transferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Goto, K. Kai, I. Miyahara, K. Hirotsu
Crystal Structure Of T. Th. Hb8 Serine Hydroxymethyltransferase
To Be Published
PubMed: search

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:31 , SER A:172 , HIS A:200 , LYS A:226 , ARG A:358 , PLP A:510 , TYR B:61 , HOH B:1846	BINDING SITE FOR RESIDUE SO4 A 2520
2	AC2	SOFTWARE	TYR A:51 , TYR A:61 , HOH A:2589 , HOH A:2597 , SER B:31 , SER B:172 , HIS B:200 , LYS B:226 , ARG B:358 , PLP B:510 , HOH B:1708	BINDING SITE FOR RESIDUE SO4 B 1520
3	AC3	SOFTWARE	SER A:93 , GLY A:94 , SER A:95 , HIS A:122 , SER A:172 , ASP A:197 , ALA A:199 , HIS A:200 , THR A:223 , HIS A:225 , LYS A:226 , SO4 A:2520 , HOH A:2530 , HOH A:2610 , TYR B:51 , GLY B:257 , GLY B:258	BINDING SITE FOR RESIDUE PLP A 510
4	AC4	SOFTWARE	TYR A:51 , GLY A:257 , GLY A:258 , SER B:93 , GLY B:94 , SER B:95 , HIS B:122 , THR B:124 , HIS B:125 , ASP B:197 , ALA B:199 , HIS B:200 , THR B:223 , HIS B:225 , LYS B:226 , SO4 B:1520 , HOH B:1526 , HOH B:1536	BINDING SITE FOR RESIDUE PLP B 510

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

Asymmetric/Biological Unit

No.	Residues
1	Phe A:252	-	Pro A:253
2	Phe B:252	-	Pro B:253

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHMT	PS00096	Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.	GLYA_THET8	218-234	2	A:218-234 B:218-234

(no "Exon" information available for 2DKJ)

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:402
 aligned with GLYA_THET8 | Q5SI56 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:402
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405  
           GLYA_THET8     6 KRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAEGYPGARYYGGCEVIDRVESLAIERAKALFGAAWANVQPHSGSQANMAVYMALMEPGDTLMGMDLAAGGHLTHGSRVNFSGKLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGASAYPRFWDFKAFREIADEVGAYLVVDMAHFAGLVAAGLHPNPLPYAHVVTSTTHKTLRGPRGGLILSNDPELGKRIDKLIFPGIQGGPLEHVIAGKAVAFFEALQPEFKEYSRLVVENAKRLAEELARRGYRIVTGGTDNHLFLVDLRPKGLTGKEAEERLDAVGITVNKNAIPFDPKPPRVTSGIRIGTPAITTRGFTPEEMPLVAELIDRALLEGPSEALREEVRRLALAHPMP 407
               SCOP domains d2dkja_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2dkjA01 A:6-32,A:285-407   2dkjA02 A:33-284 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                        2dkjA01 A:6-32,A:285-407 Aspartate Aminotransferase, domain 1                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh.ee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee.hhhh.hhhhh...hhhhhhheeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhh.eeeee...hhhhhhh...........eeeee.hhhhh....eeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dkj A   6 KRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAEGYPGARYYGGCEVIDRVESLAIERAKALFGAAWANVQPHSGSQANMAVYMALMEPGDTLMGMDLAAGGHLTHGSRVNFSGKLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGASAYPRFWDFKAFREIADEVGAYLVVDMAHFAGLVAAGLHPNPLPYAHVVTSTTHKTLRGPRGGLILSNDPELGKRIDKLIFPGIQGGPLEHVIAGKAVAFFEALQPEFKEYSRLVVENAKRLAEELARRGYRIVTGGTDNHLFLVDLRPKGLTGKEAEERLDAVGITVNKNAIPFDPKPPRVTSGIRIGTPAITTRGFTPEEMPLVAELIDRALLEGPSEALREEVRRLALAHPMP 407
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405

Chain B from PDB  Type:PROTEIN  Length:402
 aligned with GLYA_THET8 | Q5SI56 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:402
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405  
           GLYA_THET8     6 KRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAEGYPGARYYGGCEVIDRVESLAIERAKALFGAAWANVQPHSGSQANMAVYMALMEPGDTLMGMDLAAGGHLTHGSRVNFSGKLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGASAYPRFWDFKAFREIADEVGAYLVVDMAHFAGLVAAGLHPNPLPYAHVVTSTTHKTLRGPRGGLILSNDPELGKRIDKLIFPGIQGGPLEHVIAGKAVAFFEALQPEFKEYSRLVVENAKRLAEELARRGYRIVTGGTDNHLFLVDLRPKGLTGKEAEERLDAVGITVNKNAIPFDPKPPRVTSGIRIGTPAITTRGFTPEEMPLVAELIDRALLEGPSEALREEVRRLALAHPMP 407
               SCOP domains d2dkjb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2dkjB01 B:6-32,B:285-407   2dkjB02 B:33-284 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                        2dkjB01 B:6-32,B:285-407 Aspartate Aminotransferase, domain 1                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee.hhhh.hhhhh...hhhhhhheeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh...........eeeee.hhhhh....eeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhh....eeeee.hhhh.hhhhhhhhhhh..ee.eee.............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dkj B   6 KRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAEGYPGARYYGGCEVIDRVESLAIERAKALFGAAWANVQPHSGSQANMAVYMALMEPGDTLMGMDLAAGGHLTHGSRVNFSGKLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGASAYPRFWDFKAFREIADEVGAYLVVDMAHFAGLVAAGLHPNPLPYAHVVTSTTHKTLRGPRGGLILSNDPELGKRIDKLIFPGIQGGPLEHVIAGKAVAFFEALQPEFKEYSRLVVENAKRLAEELARRGYRIVTGGTDNHLFLVDLRPKGLTGKEAEERLDAVGITVNKNAIPFDPKPPRVTSGIRIGTPAITTRGFTPEEMPLVAELIDRALLEGPSEALREEVRRLALAHPMP 407
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405

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(

)

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: automated matches (28)

Thermus thermophilus HB8 [TaxId: 300852] (1)

1a	d2dkja_	A:
1b	d2dkjb_	B:

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GLYA_THET8 | Q5SI56)

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/Biological Unit
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