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Title :   STRUCTURAL BASIS OF L-PHOSPHOSERINE BINDING TO BACILLUS ALCALOPHILUS PHOSPHOSERINE AMINOTRANSFERASE

Authors :   P. Battula, A. P. Dubnovitsky, A. C. Papageorgiou

Date :   26 Jun 12 (Deposition) - 01 May 13 (Release) - 15 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

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

Reference :   P. Battula, A. P. Dubnovitsky, A. C. Papageorgiou
Structural Basis Of L-Phosphoserine Binding To Bacillus Alcalophilus Phosphoserine Aminotransferase
Acta Crystallogr. , Sect. D V. 69 804 2013
PubMed-ID: 23633589 | Reference-DOI: 10.1107/S0907444913002096

Molecule 1 - PHOSPHOSERINE AMINOTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.6.1.52
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBALC-PSAT
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BACILLUS ALCALOPHILUS
	Organism Taxid	:	1445
	Other Details	:	COVALENT BOND BETWEEN PLP AND L-PHOSPHOSERINE
	Synonym	:	PHOSPHOHYDROXYTHREONINE AMINOTRANSFERASE, PSAT

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 9)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	NA	3	Ligand/Ion	SODIUM ION
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
4	SEP	2	Mod. Residue	PHOSPHOSERINE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:9 , TRP A:102 , THR A:152 , ILE A:153 , LYS A:196 , HIS A:327 , ARG A:328 , ARG A:334 , PLP A:501 , NA A:1362 , HOH A:2564 , HOH A:2565 , HIS B:41 , ARG B:42	BINDING SITE FOR RESIDUE SEP A 500
2	AC2	SOFTWARE	GLY A:75 , ALA A:76 , SER A:77 , TRP A:102 , THR A:152 , ASP A:172 , SER A:174 , GLN A:195 , LYS A:196 , SEP A:500 , HOH A:2362 , HOH A:2565 , HOH A:2566 , ASN B:237 , THR B:238	BINDING SITE FOR RESIDUE PLP A 501
3	AC3	SOFTWARE	SER A:101 , TRP A:102 , ASN A:151 , THR A:152 , ILE A:153	BINDING SITE FOR RESIDUE CL A1361
4	AC4	SOFTWARE	TRP A:102 , ARG A:328 , SEP A:500 , HOH A:2260 , HOH A:2567	BINDING SITE FOR RESIDUE NA A1362
5	AC5	SOFTWARE	TYR A:275 , ASP A:276 , ASP A:279 , HOH A:2569	BINDING SITE FOR RESIDUE NA A1363
6	AC6	SOFTWARE	HIS A:41 , ARG A:42 , ALA B:9 , TRP B:102 , THR B:152 , ILE B:153 , LYS B:196 , HIS B:327 , ARG B:328 , ARG B:334 , PLP B:501 , NA B:1362 , HOH B:2556 , HOH B:2557	BINDING SITE FOR RESIDUE SEP B 500
7	AC7	SOFTWARE	ASN A:237 , THR A:238 , HOH A:2196 , GLY B:75 , ALA B:76 , SER B:77 , TRP B:102 , THR B:152 , ASP B:172 , SER B:174 , GLN B:195 , LYS B:196 , SEP B:500 , HOH B:2354 , HOH B:2557	BINDING SITE FOR RESIDUE PLP B 501
8	AC8	SOFTWARE	SER B:101 , TRP B:102 , ASN B:151 , THR B:152 , ILE B:153	BINDING SITE FOR RESIDUE CL B1361
9	AC9	SOFTWARE	HOH A:2422 , TRP B:102 , ARG B:328 , SEP B:500	BINDING SITE FOR RESIDUE NA B1362

(no "SS Bond" information available for 4AZJ)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:10	-	Pro A:11
2	Gly B:10	-	Pro B:11

(no "SAP(SNP)/Variant" information available for 4AZJ)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_5	PS00595	Aminotransferases class-V pyridoxal-phosphate attachment site.	SERC_BACAO	188-207	2	A:187-206 B:187-206

(no "Exon" information available for 4AZJ)

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:360
 aligned with SERC_BACAO | Q9RME2 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:360
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361
           SERC_BACAO     2 VKQVFNFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLRELLQIPNDYQILFLQGGASLQFTMLPMNLLTKGTIGNYVLTGSWSEKALKEAKLLGETHIAASTKANSYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILSRPLKVNQFGMIYAGAQKNLGPSGVTVVIVKKDLLNTKVEQVPTMLQYATHIKSDSLYNTPPTFSIYMLRNVLDWIKDLGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNVTFNLRNEELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFKENA 361
               SCOP domains d4azja_ A: Phosphoserine aminotransferase, PSAT                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........hhhhhhhhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhheeeeeee.hhhh.....hhhhh.....eeeeeee.ee....ee...........eeee..........hhhhh.eeeee..........eeeeeehhhhh......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..hhhh....eeeee..hhhhhhhhhhhhhhh.ee..........eeee.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4azj A   1 VKQVFNFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLRELLQIPNDYQILFLQGGASLQFTMLPMNLLTKGTIGNYVLTGSWSEKALKEAKLLGETHIAASTKANSYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILSRPLKVNQFGMIYAGAQKNLGPSGVTVVIVKKDLLNTKVEQVPTMLQYATHIKSDSLYNTPPTFSIYMLRNVLDWIKDLGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNVTFNLRNEELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFKENA 360
                                    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

Chain B from PDB  Type:PROTEIN  Length:358
 aligned with SERC_BACAO | Q9RME2 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:358
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353        
           SERC_BACAO     4 QVFNFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLRELLQIPNDYQILFLQGGASLQFTMLPMNLLTKGTIGNYVLTGSWSEKALKEAKLLGETHIAASTKANSYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILSRPLKVNQFGMIYAGAQKNLGPSGVTVVIVKKDLLNTKVEQVPTMLQYATHIKSDSLYNTPPTFSIYMLRNVLDWIKDLGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNVTFNLRNEELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFKENA 361
               SCOP domains d4azjb_ B: Phosphoserine aminotransferase, PSAT                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee........hhhhhhhhhhh..hhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhh..eeeeeee.hhhh.....hhhhh.....eeeeeee.ee....ee...........eeee..........hhhhh.eeeee..........eeeeeehhhhh......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..hhhh....eeeee..hhhhhhhhhhhhhhh.ee..........eeee.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4azj B   3 QVFNFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLRELLQIPNDYQILFLQGGASLQFTMLPMNLLTKGTIGNYVLTGSWSEKALKEAKLLGETHIAASTKANSYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILSRPLKVNQFGMIYAGAQKNLGPSGVTVVIVKKDLLNTKVEQVPTMLQYATHIKSDSLYNTPPTFSIYMLRNVLDWIKDLGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNVTFNLRNEELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFKENA 360
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352

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: Phosphoserine aminotransferase, PSAT (17)

Bacillus alcalophilus [TaxId: 1445] (12)

1a	d4azja_	A:
1b	d4azjb_	B:

(no "CATH Domain" information available for 4AZJ)

(no "Pfam Domain" information available for 4AZJ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SERC_BACAO | Q9RME2)

molecular function
	GO:0004648	O-phospho-L-serine:2-oxoglutarate aminotransferase activity	Catalysis of the reaction: O-phospho-L-serine + 2-oxoglutarate = 3-phosphonooxypyruvate + L-glutamate.
	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: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:0008483	transaminase activity	Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
	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:0006564	L-serine biosynthetic process	The chemical reactions and pathways resulting in the formation of 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.
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
		Gly A:10 - Pro A:11	[ RasMol ]
		Gly B:10 - Pro B:11	[ RasMol ]

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	4azj
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	2.6.1.52
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UniProtKB/Swiss-Prot
	SERC_BACAO \| Q9RME2	:	1w23 2bhx 2bi1 2bi2 2bi3 2bi5 2bi9 2bia 2bie 2big 4azk

1w23	CRYSTAL STRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE FROM BACILLUS ALCALOPHILUS
2bhx	RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE A)
2bi1	RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE B)
2bi2	RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE C)
2bi3	RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE D)
2bi5	RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE E)
2bi9	RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE F)
2bia	RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE G)
2bie	RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE H)
2big	RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE I)
4azk	STRUCTURAL BASIS OF L-PHOSPHOSERINE BINDING TO BACILLUS ALCALOPHILUS PHOSPHOSERINE AMINOTRANSFERASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

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