1KL2 - JenaLib

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Title :   CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE COMPLEXED WITH GLYCINE AND 5-FORMYL TETRAHYDROFOLATE

Authors :   V. Trivedi, A. Gupta, V. R. Jala, P. Saravanan, G. S. J. Rao, N. A. Rao, H. S. Savithri, H. S. Subramanya

Date :   11 Dec 01 (Deposition) - 10 Jul 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Shmt Plp Tetrahydrofolate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Trivedi, A. Gupta, V. R. Jala, P. Saravanan, G. S. Rao, N. A. Rao, H. S. Savithri, H. S. Subramanya
Crystal Structure Of Binary And Ternary Complexes Of Serine Hydroxymethyltransferase From Bacillus Stearothermophilus: Insights Into The Catalytic Mechanism.
J. Biol. Chem. V. 277 17161 2002
PubMed-ID: 11877399 | Reference-DOI: 10.1074/JBC.M111976200

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PRSETC
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	GEOBACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422
	Synonym	:	SERINE METHYLASE, SHMT

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	FON	2	Ligand/Ion	FOLINIC ACID
2	GLY	2	Mod. Amino Acid	GLYCINE
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:93 , GLY A:94 , ALA 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 , GLY A:601 , TYR B:51 , GLY B:257	BINDING SITE FOR RESIDUE PLP A 501
2	AC2	SOFTWARE	SER A:31 , HIS A:122 , SER A:172 , HIS A:200 , LYS A:226 , ARG A:357 , PLP A:501 , FON A:505 , TYR B:51 , TYR B:61	BINDING SITE FOR RESIDUE GLY A 601
3	AC3	SOFTWARE	TYR A:51 , GLY A:256 , GLY A:257 , SER B:93 , GLY B:94 , ALA B:95 , HIS B:122 , ALA B:171 , SER B:172 , ASP B:197 , ALA B:199 , HIS B:200 , THR B:223 , HIS B:225 , LYS B:226 , GLY B:602 , HOH B:633	BINDING SITE FOR RESIDUE PLP B 502
4	AC4	SOFTWARE	TYR A:51 , TYR A:61 , SER B:31 , HIS B:200 , LYS B:226 , ARG B:357 , PLP B:502	BINDING SITE FOR RESIDUE GLY B 602
5	AC5	SOFTWARE	LEU A:117 , GLY A:121 , HIS A:122 , LEU A:123 , SER A:172 , ASN A:341 , GLY A:601 , GLU B:53 , ARG B:58 , TYR B:60 , TYR B:61 , PHE B:251	BINDING SITE FOR RESIDUE FON A 505
6	AC6	SOFTWARE	GLU A:53 , TYR A:60 , TYR A:61 , PHE A:251 , LEU B:117 , GLY B:120 , GLY B:121 , HIS B:122 , LEU B:123 , SER B:172 , ASN B:341 , SER B:349 , PHE B:351	BINDING SITE FOR RESIDUE FON B 506

(no "SS Bond" information available for 1KL2)

(no "Cis Peptide Bond" information available for 1KL2)

(no "SAP(SNP)/Variant" information available for 1KL2)

(no "PROSITE Motif" information available for 1KL2)

(no "Exon" information available for 1KL2)

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:405
 aligned with Q7SIB6_GEOSE | Q7SIB6 from UniProtKB/TrEMBL  Length:419

    Alignment length:405
                                    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     
         Q7SIB6_GEOSE     1 MKYLPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNKYAEGYPGRRYYGGCEYVDIVEELARERAKQLFGAEHANVQPHSGAQANMAVYFTVLEHGDTVLGMNLSHGGHLTHGSPVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVAAASAYPRIIDFAKFREIADEVGAYLMVDMAHIAGLVAAGLHPNPVPYAHFVTTTTHKTLRGPRGGMILCQEQFAKQIDKAIFPGIQGGPLMHVIAAKAVAFGEALQDDFKAYAKRVVDNAKRLASALQNEGFTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITVNKNTIPYDPESPFVTSGIRIGTAAVTTRGFGLEEMDEIAAIIGLVLKNVGSEQALEEARQRVAALTD 405
               SCOP domains d1kl2a_ A: Serine hydroxymethyltransferase                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -------1kl2A01 A:8-32,A:284-405 1kl2A02 A:33-283 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                       1kl2A01 A:8-32,A:284-405 Aspartate Aminotransferase, domain 1                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee......hhhhh...hhhhhhheeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhh.eeeee...hhhhhhh...........eeeee..........eeeee...hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhhhee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kl2 A   1 MKYLPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNKYAEGYPGRRYYGGCEYVDIVEELARERAKQLFGAEHANVQPHSGAQANMAVYFTVLEHGDTVLGMNLSHGGHLTHGSPVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVAAASAYPRIIDFAKFREIADEVGAYLMVDMAHIAGLVAAGLHPNPVPYAHFVTTTTHKTLRGPRGGMILCQEQFAKQIDKAIFPGIQGGPLMHVIAAKAVAFGEALQDDFKAYAKRVVDNAKRLASALQNEGFTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITVNKNTIPYDPESPFVTSGIRIGTAAVTTRGFGLEEMDEIAAIIGLVLKNVGSEQALEEARQRVAALTD 405
                                    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

Chain B from PDB  Type:PROTEIN  Length:405
 aligned with Q7SIB6_GEOSE | Q7SIB6 from UniProtKB/TrEMBL  Length:419

    Alignment length:405
                                    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     
         Q7SIB6_GEOSE     1 MKYLPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNKYAEGYPGRRYYGGCEYVDIVEELARERAKQLFGAEHANVQPHSGAQANMAVYFTVLEHGDTVLGMNLSHGGHLTHGSPVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVAAASAYPRIIDFAKFREIADEVGAYLMVDMAHIAGLVAAGLHPNPVPYAHFVTTTTHKTLRGPRGGMILCQEQFAKQIDKAIFPGIQGGPLMHVIAAKAVAFGEALQDDFKAYAKRVVDNAKRLASALQNEGFTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITVNKNTIPYDPESPFVTSGIRIGTAAVTTRGFGLEEMDEIAAIIGLVLKNVGSEQALEEARQRVAALTD 405
               SCOP domains d1kl2b_ B: Serine hydroxymethyltransferase                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -------1kl2B01 B:8-32,B:284-405 1kl2B02 B:33-283 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                       1kl2B01 B:8-32,B:284-405 Aspartate Aminotransferase, domain 1                                                              CATH domains
           Pfam domains (1) ---SHMT-1kl2B01 B:4-380                                                                                                                                                                                                                                                                                                                                                                     ------------------------- Pfam domains (1)
           Pfam domains (2) ---SHMT-1kl2B02 B:4-380                                                                                                                                                                                                                                                                                                                                                                     ------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee......hhhhh...hhhhhhheeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh...........eeeee..........eeeeehhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee......hhhhhhhhhhhhhee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kl2 B   1 MKYLPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNKYAEGYPGRRYYGGCEYVDIVEELARERAKQLFGAEHANVQPHSGAQANMAVYFTVLEHGDTVLGMNLSHGGHLTHGSPVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVAAASAYPRIIDFAKFREIADEVGAYLMVDMAHIAGLVAAGLHPNPVPYAHFVTTTTHKTLRGPRGGMILCQEQFAKQIDKAIFPGIQGGPLMHVIAAKAVAFGEALQDDFKAYAKRVVDNAKRLASALQNEGFTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITVNKNTIPYDPESPFVTSGIRIGTAAVTTRGFGLEEMDEIAAIIGLVLKNVGSEQALEEARQRVAALTD 405
                                    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

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: Serine hydroxymethyltransferase (50)

Bacillus stearothermophilus [TaxId: 1422] (39)

1a	d1kl2a_	A:
1b	d1kl2b_	B:

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PLP_aminotran (240)

Family: SHMT (45)

Geobacillus stearothermophilus (Bacillus stearothermophilus) (38)

1a	SHMT-1kl2B01	B:4-380
1b	SHMT-1kl2B02	B:4-380

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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/Biological Unit
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	1kl2
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	2.1.2.1
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1kkj	1KKJ IS THE NATIVE PROTEIN (WITHOUT SUBSTRATE)
1kkp	1KKP IS SHMT COMPLEXED WITH SERINE SUBSTRATE
1kl1	1KL1 IS SHMT COMPLEXED WITH GLYCINE SUBSTRATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (2, 4)

Pfam Domains (1, 2)

Gene Ontology (12, 12)

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