2BI9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   RADIATION DAMAGE OF THE SCHIFF BASE IN PHOSPHOSERINE AMINOTRANSFERASE (STRUCTURE F)

Authors :   A. P. Dubnovitsky, R. B. G. Ravelli, A. N. Popov, A. C. Papageorgiou

Date :   20 Jan 05 (Deposition) - 19 May 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.73

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

Keywords :   Transferase, Aminotransferase, Pyridoxal-5'-Phosphate, Radiation Damage (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. P. Dubnovitsky, R. B. G. Ravelli, A. N. Popov, A. C. Papageorgiou
Strain Relief At The Active Site Of Phosphoserine Aminotransferase Induced By Radiation Damage.
Protein Sci. V. 14 1498 2005
PubMed-ID: 15883191 | Reference-DOI: 10.1110/PS.051397905

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
	Organism Scientific	:	BACILLUS ALCALOPHILUS
	Organism Taxid	:	1445
	Other Details	:	PYRIDOXAL-5'-PHOSPHATE LINKED TO 196

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 14)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	CL	4	Ligand/Ion	CHLORIDE ION
3	MG	4	Ligand/Ion	MAGNESIUM ION
4	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:256 , HOH A:2177 , HOH A:2181 , HOH A:2182 , GLU B:51 , HOH B:2064	BINDING SITE FOR RESIDUE MG A1362
02	AC2	SOFTWARE	ASP A:344 , HOH A:2260 , ASP B:66 , HOH B:2084 , HOH B:2085 , HOH B:2181	BINDING SITE FOR RESIDUE MG A1363
03	AC3	SOFTWARE	SER A:101 , TRP A:102 , ASN A:151 , THR A:152 , ILE A:153 , TYR A:154 , HOH A:2123	BINDING SITE FOR RESIDUE CL A1364
04	AC4	SOFTWARE	TRP A:102 , ARG A:334 , HOH A:2008	BINDING SITE FOR RESIDUE CL A1365
05	AC5	SOFTWARE	HOH A:2200 , HOH A:2202 , HOH B:2110 , HOH B:2242 , HOH B:2246 , HOH B:2247	BINDING SITE FOR RESIDUE MG B1362
06	AC6	SOFTWARE	ASP B:256 , HOH B:2215 , HOH B:2220 , HOH B:2222	BINDING SITE FOR RESIDUE MG B1363
07	AC7	SOFTWARE	SER B:101 , TRP B:102 , ASN B:151 , THR B:152 , ILE B:153	BINDING SITE FOR RESIDUE CL B1364
08	AC8	SOFTWARE	TRP B:102 , ILE B:153 , ARG B:334 , HOH B:2013 , HOH B:2293	BINDING SITE FOR RESIDUE CL B1365
09	AC9	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 , HOH A:2271 , HOH A:2272 , ASN B:237 , THR B:238 , HOH B:2206	BINDING SITE FOR RESIDUE PLP A1361
10	BC1	SOFTWARE	ASP A:279 , LYS A:291 , HOH A:2273 , HOH A:2274 , GLU B:269 , ILE B:343 , HOH B:2236	BINDING SITE FOR RESIDUE 1PE A1366
11	BC2	SOFTWARE	ASN A:237 , THR A:238 , HOH A:2170 , GLY B:75 , ALA B:76 , SER B:77 , PHE B:80 , TRP B:102 , THR B:152 , ASP B:172 , SER B:174 , GLN B:195 , LYS B:196 , HOH B:2316 , HOH B:2317	BINDING SITE FOR RESIDUE PLP B1361
12	BC3	SOFTWARE	GLN A:159 , LYS A:291 , ARG A:294 , LEU A:296 , HOH A:2277	BINDING SITE FOR RESIDUE PEG A1367
13	BC4	SOFTWARE	GLU A:104 , LYS A:123	BINDING SITE FOR RESIDUE PEG A1368
14	BC5	SOFTWARE	GLN B:159 , TYR B:275 , LYS B:291 , GLY B:292 , ARG B:294 , LEU B:296 , HOH B:2260	BINDING SITE FOR RESIDUE PEG B1366

(no "SS Bond" information available for 2BI9)

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 2BI9)

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 2BI9)

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 d2bi9a_ A: Phosphoserine aminotransferase, PSAT                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ---------------2bi9A01 A:16-257 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                              2bi9A02 A:258-360 Aspartate Aminotransferase, domain 1                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........hhhhhhhhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhh..eeeeeee.hhhh.....hhhhh.....eeeeeee.ee....ee...........eeee..........hhhhh.eeeee..........eeeeeehhhhh......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee..hhhh....eeeee..hhhhhhhhhhhhhhh.ee..........eeee.....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bi9 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:356
 aligned with SERC_BACAO | Q9RME2 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:359
                                    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         
           SERC_BACAO     3 KQVFNFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLRELLQIPNDYQILFLQGGASLQFTMLPMNLLTKGTIGNYVLTGSWSEKALKEAKLLGETHIAASTKANSYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILSRPLKVNQFGMIYAGAQKNLGPSGVTVVIVKKDLLNTKVEQVPTMLQYATHIKSDSLYNTPPTFSIYMLRNVLDWIKDLGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNVTFNLRNEELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFKENA 361
               SCOP domains d2bi9b_ B: Phosphoserine aminotransferase, PSAT                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains --------------2bi9B01 B:16-257 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                              2bi9B02 B:258-360 Aspartate Aminotransferase, domain 1                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee........hhhhhhhhhhh..hhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhheeeeeee.hhhh.....hhhhh.....eeeeeee.ee....ee...........eeee..........hhhhh.eeeee..........eeeeee....---....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee..hhhh....eeeeee.hhhhhhhhhhhhhhh.ee..........eeee.....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5 ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bi9 B   2 KQVFNFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLRELLQIPNDYQILFLQGGASLQFTMLPMNLLTKGTIGNYVLTGSWSEKALKEAKLLGETHIAASTKANSYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILSRPLKVNQFGMIYAGAQKNLGPSGVTVVIVKKDLL---VEQVPTMLQYATHIKSDSLYNTPPTFSIYMLRNVLDWIKDLGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNVTFNLRNEELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFKENA 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         
                                                                                                                                                                                                                                             213 217

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	d2bi9a_	A:
1b	d2bi9b_	B:

(no "Pfam Domain" information available for 2BI9)

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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		1PE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PEG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PLP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:10 - Pro A:11	[ RasMol ]
		Gly B:10 - Pro B:11	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2bi9
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	SERC_BACAO \| Q9RME2
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.6.1.52
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	SERC_BACAO \| Q9RME2
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 14)

Sites (14, 14)

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 (2, 4)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File