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Title :   CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE FROM CAMPYLOBACTER JEJUNI

Authors :   S. M. Anderson, Z. Wawrzak, O. Onopriyenko, J. Hasseman, W. F. Anderson A. Savchenko, Center For Structural Genomics Of Infectious Di (Csgid)

Date :   14 May 10 (Deposition) - 26 May 10 (Release) - 14 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Campylobacter, Alpha Beta Class, 3-Layer(Aba) Sandwich, Csgid, Transferase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. M. Anderson, Z. Wawrzak, O. Onopriyenko, J. Hasseman, W. F. Anderson, A. Savchenko, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Serine Hydroxymethyltransferase From Campylobacter Jejuni
To Be Published
PubMed: search

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)-MAGIC
	Expression System Taxid	:	469008
	Gene	:	GLYA, CJ0402
	Organism Scientific	:	CAMPYLOBACTER JEJUNI
	Organism Taxid	:	197
	Synonym	:	SERINE METHYLASE, SHMT

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 41)

No.	Name	Count	Type	Full Name
1	MSE	26	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	15	Ligand/Ion	SULFATE ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:92 , GLY A:93 , SER A:94 , THR A:221 , ARG A:230 , SO4 A:416 , HOH A:570 , HOH A:599 , HOH A:614 , TYR B:50 , GLY B:255 , GLY B:256	BINDING SITE FOR RESIDUE SO4 A 415
02	AC2	SOFTWARE	THR A:221 , HIS A:223 , LYS A:224 , ARG A:230 , GLY A:231 , SO4 A:415	BINDING SITE FOR RESIDUE SO4 A 416
03	AC3	SOFTWARE	SER A:30 , SER A:170 , HIS A:198 , LYS A:224 , ARG A:356 , TYR B:50 , TYR B:60	BINDING SITE FOR RESIDUE SO4 A 417
04	AC4	SOFTWARE	ASN A:-1 , ALA A:0 , MSE A:1 , SER A:2 , GLU B:40 , ARG B:411	BINDING SITE FOR RESIDUE SO4 A 418
05	AC5	SOFTWARE	VAL A:342 , PRO A:343 , GLY A:344 , GLU A:345 , HOH A:494 , HOH A:656 , LYS B:370	BINDING SITE FOR RESIDUE SO4 A 419
06	AC6	SOFTWARE	LYS A:78 , ASN A:82 , CYS A:83 , LYS A:84 , HOH A:501 , HOH B:460 , HOH B:539	BINDING SITE FOR RESIDUE SO4 A 420
07	AC7	SOFTWARE	CYS A:22 , PHE A:33 , ARG A:365 , PHE A:406 , ILE A:407 , ILE A:408 , TYR A:409	BINDING SITE FOR RESIDUE SO4 A 421
08	AC8	SOFTWARE	ASP A:318 , ARG A:319 , GLU A:320 , PHE A:321	BINDING SITE FOR RESIDUE SO4 A 422
09	AC9	SOFTWARE	TYR A:50 , GLY A:255 , GLY A:256 , SER B:92 , GLY B:93 , SER B:94 , ARG B:230 , SO4 B:416 , HOH B:550 , HOH B:572 , HOH B:628 , HOH B:629	BINDING SITE FOR RESIDUE SO4 B 415
10	BC1	SOFTWARE	THR B:221 , HIS B:223 , LYS B:224 , ARG B:230 , GLY B:231 , SO4 B:415 , HOH B:540 , HOH B:550	BINDING SITE FOR RESIDUE SO4 B 416
11	BC2	SOFTWARE	TYR A:50 , TYR A:60 , SER B:30 , SER B:170 , HIS B:198 , LYS B:224 , ARG B:356	BINDING SITE FOR RESIDUE SO4 B 417
12	BC3	SOFTWARE	ARG B:174	BINDING SITE FOR RESIDUE SO4 B 418
13	BC4	SOFTWARE	LEU B:35 , GLU B:37 , PHE B:271	BINDING SITE FOR RESIDUE SO4 B 419
14	BC5	SOFTWARE	GLU A:40 , ARG A:411 , ALA B:0 , MSE B:1 , SER B:2	BINDING SITE FOR RESIDUE SO4 B 420
15	BC6	SOFTWARE	ASP A:186 , HOH A:571 , ARG B:182 , ASP B:186 , HOH B:557	BINDING SITE FOR RESIDUE SO4 B 421

(no "SS Bond" information available for 3N0L)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:212	-	Pro A:213
2	Phe A:250	-	Pro A:251
3	Phe B:212	-	Pro B:213
4	Phe B:250	-	Pro B:251

(no "SAP(SNP)/Variant" information available for 3N0L)

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_CAMJE	216-232	2	A:216-232 B:216-232

(no "Exon" information available for 3N0L)

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:400
 aligned with GLYA_CAMJE | P24531 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:416
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408      
           GLYA_CAMJE     - --MSLEMFDKEIFDLTNKELERQCEGLEMIASENFTLPEVMEVMGSILTNKYAEGYPGKRYYGGCEFVDEIETLAIERCKKLFNCKFANVQPNSGSQANQGVYAALINPGDKILGMDLSHGGHLTHGAKVSSSGKMYESCFYGVELDGRIDYEKVREIAKKEKPKLIVCGASAYARVIDFAKFREIADEIGAYLFADIAHIAGLVVAGEHPSPFPYAHVVSSTTHKTLRGPRGGIIMTNDEELAKKINSAIFPGIQGGPLMHVIAAKAVGFKFNLSDEWKVYAKQVRTNAQVLANVLMDRKFKLVSDGTDNHLVLMSFLDREFSGKDADLALGNAGITANKNTVPGEIRSPFITSGLRLGTPALTARGFKEKEMEIVSNYIADILDDVNNEKLQENIKQELKKLASNFIIYERAMF 414
               SCOP domains d3n0la_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee..----------------...eeeee........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhh.eeeee...hhhhhhh...........eeeee..........eeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee......hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n0l A  -1 NAmSLEmFDKEIFDLTNKELERQCEGLEmIASENFTLPEVmEVmGSILTNKYAEGYPGKRYYGGCEFVDEIETLAIERCKKLFNCKFANVQPNSGSQANQGVYAALINPGDKILGmDL----------------KmYESCFYGVELDGRIDYEKVREIAKKEKPKLIVCGASAYARVIDFAKFREIADEIGAYLFADIAHIAGLVVAGEHPSPFPYAHVVSSTTHKTLRGPRGGIImTNDEELAKKINSAIFPGIQGGPLmHVIAAKAVGFKFNLSDEWKVYAKQVRTNAQVLANVLmDRKFKLVSDGTDNHLVLmSFLDREFSGKDADLALGNAGITANKNTVPGEIRSPFITSGLRLGTPALTARGFKEKEmEIVSNYIADILDDVNNEKLQENIKQELKKLASNFIIYERAmF 414
                              |   |  8        18        28        38|  |    48        58        68        78        88        98       108     | | -         -    || 138       148       158       168       178       188       198       208       218       228      |238       248       258|      268       278       288       298       308     | 318       328       338       348       358       368   |   378       388       398       408    | 
                              |   |                    27-MSE      39-MSE                                                                    114-MSE            133|                                                                                                  235-MSE                 259-MSE                              296-MSE           314-MSE                                                   372-MSE                                  413-MSE
                              1-MSE                                   42-MSE                                                                   116               134-MSE                                                                                                                                                                                                                                                                                    
                                  5-MSE

Chain B from PDB  Type:PROTEIN  Length:401
 aligned with GLYA_CAMJE | P24531 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:417
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       
           GLYA_CAMJE     - ---MSLEMFDKEIFDLTNKELERQCEGLEMIASENFTLPEVMEVMGSILTNKYAEGYPGKRYYGGCEFVDEIETLAIERCKKLFNCKFANVQPNSGSQANQGVYAALINPGDKILGMDLSHGGHLTHGAKVSSSGKMYESCFYGVELDGRIDYEKVREIAKKEKPKLIVCGASAYARVIDFAKFREIADEIGAYLFADIAHIAGLVVAGEHPSPFPYAHVVSSTTHKTLRGPRGGIIMTNDEELAKKINSAIFPGIQGGPLMHVIAAKAVGFKFNLSDEWKVYAKQVRTNAQVLANVLMDRKFKLVSDGTDNHLVLMSFLDREFSGKDADLALGNAGITANKNTVPGEIRSPFITSGLRLGTPALTARGFKEKEMEIVSNYIADILDDVNNEKLQENIKQELKKLASNFIIYERAMF 414
               SCOP domains d3n0lb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----SHMT-3n0lB01 B:3-379                                                                                                                                                                                                                                                                                                                                                                     ----------------------------------- Pfam domains (1)
           Pfam domains (2) -----SHMT-3n0lB02 B:3-379                                                                                                                                                                                                                                                                                                                                                                     ----------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee..----------------...eeeee........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh...........eeeee..........eeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee......hhhhhhhhhhhh.ee.ee..............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n0l B  -2 SNAmSLEmFDKEIFDLTNKELERQCEGLEmIASENFTLPEVmEVmGSILTNKYAEGYPGKRYYGGCEFVDEIETLAIERCKKLFNCKFANVQPNSGSQANQGVYAALINPGDKILGmDL----------------KmYESCFYGVELDGRIDYEKVREIAKKEKPKLIVCGASAYARVIDFAKFREIADEIGAYLFADIAHIAGLVVAGEHPSPFPYAHVVSSTTHKTLRGPRGGIImTNDEELAKKINSAIFPGIQGGPLmHVIAAKAVGFKFNLSDEWKVYAKQVRTNAQVLANVLmDRKFKLVSDGTDNHLVLmSFLDREFSGKDADLALGNAGITANKNTVPGEIRSPFITSGLRLGTPALTARGFKEKEmEIVSNYIADILDDVNNEKLQENIKQELKKLASNFIIYERAmF 414
                               |   | 7        17        27        37 |  |   47        57        67        77        87        97       107      | |-         -     ||137       147       157       167       177       187       197       207       217       227       237       247       257 |     267       277       287       297       307      |317       327       337       347       357       367    |  377       387       397       407     | 
                               |   |                    27-MSE      39-MSE                                                                    114-MSE            133|                                                                                                  235-MSE                 259-MSE                              296-MSE           314-MSE                                                   372-MSE                                  413-MSE
                               1-MSE                                   42-MSE                                                                   116               134-MSE                                                                                                                                                                                                                                                                                    
                                   5-MSE

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: automated matches (163)

Protein domain: automated matches (163)

Campylobacter jejuni [TaxId: 197] (2)

1a	d3n0la_	A:
1b	d3n0lb_	B:

(no "CATH Domain" information available for 3N0L)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PLP_aminotran (240)

Family: SHMT (45)

Campylobacter jejuni (1)

1a	SHMT-3n0lB01	B:3-379
1b	SHMT-3n0lB02	B:3-379

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GLYA_CAMJE | P24531)

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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	Cis Peptide Bonds
		Phe A:212 - Pro A:213	[ RasMol ]
		Phe A:250 - Pro A:251	[ RasMol ]
		Phe B:212 - Pro B:213	[ RasMol ]
		Phe B:250 - Pro B:251	[ RasMol ]

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