1BJO - JenaLib

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Title :   THE STRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE FROM E. COLI IN COMPLEX WITH ALPHA-METHYL-L-GLUTAMATE

Authors :   G. Hester, W. Stark, J. N. Jansonius

Date :   25 Jun 98 (Deposition) - 04 Nov 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Aminotransferase, L-Serine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Hester, W. Stark, M. Moser, J. Kallen, Z. Markovic-Housley, J. N. Jansonius
Crystal Structure Of Phosphoserine Aminotransferase From Escherichia Coli At 2. 3 A Resolution: Comparison Of The Unligated Enzyme And A Complex With Alpha-Methyl-L-Glutamate.
J. Mol. Biol. V. 286 829 1999
PubMed-ID: 10024454 | Reference-DOI: 10.1006/JMBI.1998.2506
(for further references see the PDB file header)

Molecule 1 - PHOSPHOSERINE AMINOTRANSFERASE
	Chains	:	A
	EC Number	:	2.6.1.52
	Engineered	:	YES
	Gene	:	SERC
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	IN CHAIN A AN EXTERNAL ALDIMINE INTERMEDIATE BETWEEN PYRIDOXAL-5'-PHOSPHATE AND ALPHA-METHYL-L-GLUTAMATE IS NON-COVALENTLY BOUND WHILE IN CHAIN B A PYRIDOXAL-5'-PHOSPHATE MOLECULE IS COVALENTLY BOUND IN AN ALDIMINE LINKAGE TO A LYSINE SIDE CHAIN
	Synonym	:	PSAT

Molecule 2 - PHOSPHOSERINE AMINOTRANSFERASE
	Chains	:	B
	EC Number	:	2.6.1.52
	Engineered	:	YES
	Gene	:	SERC
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	IN CHAIN A AN EXTERNAL ALDIMINE INTERMEDIATE BETWEEN PYRIDOXAL-5'-PHOSPHATE AND ALPHA-METHYL-L-GLUTAMATE IS NON-COVALENTLY BOUND WHILE IN CHAIN B A PYRIDOXAL-5'-PHOSPHATE MOLECULE IS COVALENTLY BOUND IN AN ALDIMINE LINKAGE TO A LYSINE SIDE CHAIN
	Synonym	:	PSAT

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	GAM	1	Ligand/Ion	ALPHA-METHYL-L-GLUTAMIC ACID
2	LLP	1	Mod. Amino Acid	2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:75 , GLY A:76 , ARG A:77 , TRP A:102 , THR A:153 , ASP A:174 , SER A:176 , GLN A:197 , LYS A:198 , GAM A:364 , ASN B:239 , THR B:240	BINDING SITE FOR RESIDUE PLP A 363
2	AC2	SOFTWARE	SER A:9 , GLY A:10 , TRP A:102 , THR A:153 , ILE A:154 , LYS A:198 , HIS A:328 , ARG A:335 , PLP A:363 , HOH A:365 , ARG B:42	BINDING SITE FOR RESIDUE GAM A 364
3	PPA	UNKNOWN	LYS A:198	PLP BINDING SITE.
4	PPB	UNKNOWN	LLP B:198	PLP BINDING SITE.

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

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 1BJO)

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_ECOLI	189-208	2	A:189-208 B:189-208

(no "Exon" information available for 1BJO)

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_ECOLI | P23721 from UniProtKB/Swiss-Prot  Length:362

    Alignment length: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       362
           SERC_ECOLI     3 QIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362
               SCOP domains d1bjoa_ A: Phosphoserine aminotransferase, PSAT                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------1bjoA01 A:17-258 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                              1bjoA02 A:259-361 Aspartate Aminotransferase, domain 1                                                 - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhhhh....hhh............hhhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhh..eeeeee.eeee..eeee..hhh.........eee......................eeee...........hhh..eeeee..........eeeeeehhh.........hhh.hhhhhh.........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.........hhh....eeee....hhhhhhhhhhhhh..............eeee......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1bjo A   3 QIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKRNRSRMNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362
                                    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       362

Chain B from PDB  Type:PROTEIN  Length:360
 aligned with SERC_ECOLI | P23721 from UniProtKB/Swiss-Prot  Length:362

    Alignment length: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       362
           SERC_ECOLI     3 QIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362
               SCOP domains d1bjob_ B: Phosphoserine aminotransferase, PSAT                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------1bjoB01 B:17-258 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                              1bjoB02 B:259-361 Aspartate Aminotransferase, domain 1                                                 - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhhhh....hhh............hhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhh..eeeeee.eeee..eeee..hhh.........eee......................eeee...........hhh..eeeee..........eeeeeehhh.........hhh.hhhhhh.........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.........hhh....eeee....hhhhhhhhhhhhh..............eeee......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1bjo B   3 QIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPIDVSRYGVIYAGAQkNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKRNRSRMNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362
                                    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       362
                                                                                                                                                                                                                             198-LLP

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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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)

Escherichia coli [TaxId: 562] (2)

1a	d1bjoa_	A:
1b	d1bjob_	B:

(no "Pfam Domain" information available for 1BJO)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SERC_ECOLI | P23721)

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: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:0033359	lysine biosynthetic process via diaminopimelate and N-succinyl-2-amino-6-ketopimelate	The chemical reactions and pathways resulting in the formation of lysine, via the intermediates diaminopimelate and N-succinyl-2-amino-6-ketopimelate; in this pathway tetrahydrodipicolinate is converted to meso-diaminopimelate in four enzymatic steps.
	GO:0042823	pyridoxal phosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
	GO:0008615	pyridoxine biosynthetic process	The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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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	1bjo
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(no "Related Entries Specified in the PDB File" available for 1BJO)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (1, 2)

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