2W7K - JenaLib

Title :   CRYSTAL STRUCTURE OF Y61ABSSHMT L-SERINE EXTERNAL ALDIMINE

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

Date :   22 Dec 08 (Deposition) - 18 Aug 10 (Release) - 18 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.42

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

Keywords :   Transferase, One-Carbon Metabolism, Plp-Dependent Enzymes (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. S. Bhavani, V. Rajaram, S. Bisht, P. Kaul, V. Prakash, M. R. N. Murthy N. Appaji Rao, H. S. Savithri
Importance Of Tyrosine Residues Of Bacillus Stearothermophilus Serine Hydroxymethyltransferase In Cofactor Binding And L-Allo-Thr Cleavage.
Febs J. V. 275 4606 2008
PubMed-ID: 18699779 | Reference-DOI: 10.1111/J.1742-4658.2008.06603.X

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

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

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
	(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:406
 aligned with Q7SIB6_GEOSE | Q7SIB6 from UniProtKB/TrEMBL  Length:419

    Alignment length:407
                                    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 MKYLPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNKYAEGYPGRRYYGGCEYVDIVEELARERAKQLFGAEHANVQPHSGAQANMAVYFTVLEHGDTVLGMNLSHGGHLTHGSPVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVAAASAYPRIIDFAKFREIADEVGAYLMVDMAHIAGLVAAGLHPNPVPYAHFVTTTTHKTLRGPRGGMILCQEQFAKQIDKAIFPGIQGGPLMHVIAAKAVAFGEALQDDFKAYAKRVVDNAKRLASALQNEGFTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITVNKNTIPYDPESPFVTSGIRIGTAAVTTRGFGLEEMDEIAAIIGLVLKNVGSEQALEEARQRVAALTDPT 407
               SCOP domains d2w7ka_ A: Serine hydroxymethyltransferase                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2w7kA01 A:1-32,A:284-405        2w7kA02 A:33-283 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                       2w7kA01 A:1-32,A:284-405 Aspartate Aminotransferase, domain 1                                                             -- CATH domains
               Pfam domains ---SHMT-2w7kA01 A:4-380                                                                                                                                                                                                                                                                                                                                                                     --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee......hhhhh...hhhhhhheeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhh.eeeee...hhhhhhh...........eeeee..........eeeeehhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhhhee.eee.............eeeeehhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.-. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w7k A   1 MKYLPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNKYAEGYPGRRYAGGCEYVDIVEELARERAKQLFGAEHANVQPHSGAQANMAVYFTVLEHGDTVLGMNLSHGGHLTHGSPVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVAAASAYPRIIDFAKFREIADEVGAYLMVDMAHIAGLVAAGLHPNPVPYAHFVTTTTHKTLRGPRGGMILCQEQFAKQIDKAIFPGIQGGPLMHVIAAKAVAFGEALQDDFKAYAKRVVDNAKRLASALQNEGFTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITVNKNTIPYDPESPFVTSGIRIGTAAVTTRGFGLEEMDEIAAIIGLVLKNVGSEQALEEARQRVAALTD-S 601
                                    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    | |
                                                                                                                                                                                                                                                                                                                                                                                                                                              405 |
                                                                                                                                                                                                                                                                                                                                                                                                                                                601

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (2, 2)

Pfam Domains (1, 1)

Gene Ontology (12, 12)

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.

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Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

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
2vgw	CRYSTAL STRUCTURE OF E53QBSSHMT OBTAINED IN THE PRESENCE OF GLYCINE AND 5-FOMYL TETRAHYDROFOLATE
2vi8	CRYSTAL STRUCTURE OF S172ABSSHMT INTERNAL ALDIMINE
2vi9	CRYSTAL STRUCTURE OF S172ABSSHMT GLYCINE EXTERNAL ALDIMINE
2via	CRYSTAL STRUCTURE OF S172ABSSHMT L-SERINE EXTERNAL ALDIMINE
2vib	CRYSTAL STRUCTURE OF S172ABSSHMT OBTAINED IN THE PRESENCE OF L-ALLO-THR
2vmn	CRYSTAL STRUCTURE OF N341ABSSHMT INTERNAL ALDIMINE
2vmo	CRYSTAL STRUCTURE OF N341ABSSHMT GLY EXTERNAL ALDIMINE
2vmp	CRYSTAL STRUCTURE OF N341ABSSHMT L-SER EXTERNAL ALDIMINE
2vmq	STRUCTURE OF N341ABSSHMT CRYSTALLIZED IN THE PRESENCE OF L- ALLO-THR
2vmr	CRYSTAL STRUCTURE OF Y60ABSSHMT INTERNAL ALDIMINE
2vms	CRYSTAL STRUCTURE OF Y60ABSSHMT CRYSTALLIZED IN THE PRESENCE OF GLYCINE
2vmt	CRYSTAL STRUCTURE OF Y60ABSSHMT L-SER EXTERNAL ALDIMINE
2vmu	CRYSTAL STRUCTURE OF Y60ABSSHMT CRYSTALLIZED IN THE PRESENCE OF L-ALLO-THR
2vmv	CRYSTAL STRUCTURE OF F351GBSSHMT INTERNAL ALDIMINE
2vmw	CRYSTAL STRUCTURE OF F351GBSSHMT IN COMPLEX WITH L-SER
2vmx	CRYSTAL STRUCTURE OF F351GBSSHMT IN COMPLEX WITH L-ALLO-THR
2vmy	CRYSTAL STRUCTURE OF F351GBSSHMT IN COMPLEX WITH GLY AND FTHF
2vmz	CRYSTAL STRUCTURE OF F351GBSSHMT IN COMPLEX WITH GLY
2w7d	CRYSTAL STRUCTURE OF Y51FBSSHMT INTERNAL ALDIMINE
2w7e	CRYSTAL STRUCTURE OF Y51FBSSHMT OBTAINED IN THE PRESENCE OF GLYCINE
2w7f	CRYSTAL STRUCTURE OF Y51FBSSHMT L-SER EXTERNAL ALDIMINE
2w7g	CRYSTAL STRUCTURE OF Y51FBSSHMT L-ALLO- THREONINE EXTRNAL ALDIMINE
2w7h	CRYSTAL STRUCTURE OF Y51FBSSHMT OBTAINED IN THE PRESENCE OF GLY AND 5-FORMYL TETRAHYDROFOLATE
2w7i	CRYSTAL STRUCTURE OF Y61ABSSHMT INTERNAL ALDIMINE

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