2BKW - JenaLib

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   YEAST ALANINE:GLYOXYLATE AMINOTRANSFERASE YFL030W

Authors :   P. Meyer, D. Liger, N. Leulliot, S. Quevillon-Cheruel, C. Z. Zhou, F. Bo J. L. Ferrer, A. Poupon, J. Janin, H. Van Tilbeurgh

Date :   21 Feb 05 (Deposition) - 02 Nov 05 (Release) - 18 Nov 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.57

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

Keywords :   Analine-Glyoxylate Aminotransferase, Pyridoxal-5-Phosphate, Sad, Glycolate Pathway, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Meyer, D. Liger, N. Leulliot, S. Quevillon-Cheruel, C. Z. Zhou, F. Borel, J. L. Ferrer, A. Poupon, J. Janin, H. Van Tilbeurgh
Crystal Structure And Confirmation Of The Alanine:Glyoxylate Aminotransferase Activity Of The Yfl030W Yeast Protein
Biochimie V. 87 1041 2005
PubMed-ID: 16226833 | Reference-DOI: 10.1016/J.BIOCHI.2005.09.001

Molecule 1 - ALANINE-GLYOXYLATE AMINOTRANSFERASE 1
	Chains	:	A
	EC Number	:	2.6.1.44
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET9
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE S288C
	Organism Taxid	:	559292
	Other Details	:	PYRIDOXAL 5'-PHOSPHATE LINK TO A 201, GLYOXYLATE

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	GLV	1	Ligand/Ion	GLYOXYLIC ACID
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (3, 16)

No.	Name	Count	Type	Full Name
1	GLV	2	Ligand/Ion	GLYOXYLIC ACID
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:67 , GLY A:68 , THR A:69 , TRP A:72 , PHE A:97 , THR A:144 , VAL A:146 , THR A:148 , ASP A:175 , VAL A:177 , CYS A:178 , GLN A:200 , LYS A:201 , TYR A:255 , THR A:258 , GLV A:1384	BINDING SITE FOR RESIDUE PLP A1201
2	AC2	SOFTWARE	HIS A:31 , THR A:148 , TYR A:255 , ARG A:354 , PLP A:1201	BINDING SITE FOR RESIDUE GLV A1384

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

Asymmetric Unit

No.	Residues
1	Gly A:12	-	Pro A:13
2	Tyr A:309	-	Pro A:310

(no "SAP(SNP)/Variant" information available for 2BKW)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_5	PS00595	Aminotransferases class-V pyridoxal-phosphate attachment site.	AGX1_YEAST	192-212	1	A:192-212

Biological Unit 1 (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.	AGX1_YEAST	192-212	2	A:192-212

Asymmetric Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YFL030W	1	YFL030W.1	VI:76829-77986	1158	AGX1_YEAST	1-385	385	1	A:3-384	382

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:382
 aligned with AGX1_YEAST | P43567 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:382
                                    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       372       382  
           AGX1_YEAST     3 KSVDTLLIPGPIILSGAVQKALDVPSLGHTSPEFVSIFQRVLKNTRAVFKSAAASKSQPFVLAGSGTLGWDIFASNFILSKAPNKNVLVVSTGTFSDRFADCLRSYGAQVDVVRPLKIGESVPLELITEKLSQNSYGAVTVTHVDTSTAVLSDLKAISQAIKQTSPETFFVVDAVCSIGCEEFEFDEWGVDFALTASQKAIGAPAGLSISLCSSRFMDYALNDSKNGHVHGYFSSLRRWTPIMENYEAGKGAYFATPPVQLINSLDVALKEILEEGLHKRWDLHREMSDWFKDSLVNGLQLTSVSRYPSNMSAHGLTAVYVADPPDVIAFLKSHGVVIAGGIHKDIGPKYIRIGHMGVTACNKNLPYMKNCFDLIKLALQRK 384
               SCOP domains d2bkwa1 A:3-384 Alanine-glyoxylate aminotransferase                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........hhhhhhh.........hhhhhhhhhhhhhhhhhhh..hhhhh.eeeeee...hhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhh...eeeee.ee....ee.hhhhhhhhhhhhh...eeeee..................eeeee..........eeeeeehhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.............eeee..hhhhhhhhhhhh.ee........hhh.eeee..hhhhh.....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-384 UniProt: 1-385 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                             Transcript 1
                 2bkw A   3 KSVDTLLIPGPIILSGAVQKALDVPSLGHTSPEFVSIFQRVLKNTRAVFKSAAASKSQPFVLAGSGTLGWDIFASNFILSKAPNKNVLVVSTGTFSDRFADCLRSYGAQVDVVRPLKIGESVPLELITEKLSQNSYGAVTVTHVDTSTAVLSDLKAISQAIKQTSPETFFVVDAVCSIGCEEFEFDEWGVDFALTASQKAIGAPAGLSISLCSSRFmDYALNDSKNGHVHGYFSSLRRWTPImENYEAGKGAYFATPPVQLINSLDVALKEILEEGLHKRWDLHREmSDWFKDSLVNGLQLTSVSRYPSNmSAHGLTAVYVADPPDVIAFLKSHGVVIAGGIHKDIGPKYIRIGHmGVTACNKNLPYmKNCFDLIKLALQRK 384
                                    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       372       382  
                                                                                                                                                                                                                                                  219-MSE                   245-MSE                                     289-MSE                 313-MSE                                      358-MSE     370-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Protein Domains( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: PLP-dependent transferase-like (627)

Superfamily: PLP-dependent transferases (625)

Family: Cystathionine synthase-like (64)

Protein domain: Alanine-glyoxylate aminotransferase (4)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (1)

d2bkwa1

A:3-384

(no "CATH Domain" information available for 2BKW)

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

Asymmetric Unit(hide GO term definitions)

Chain A (AGX1_YEAST | P43567)

molecular function
	GO:0008453	alanine-glyoxylate transaminase activity	Catalysis of the reaction: L-alanine + glyoxylate = pyruvate + glycine.
	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: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:0006545	glycine biosynthetic process	The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
	GO:0019265	glycine biosynthetic process, by transamination of glyoxylate	The chemical reactions and pathways resulting in the formation of glycine by the transamination of glyoxylate.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:12 - Pro A:13	[ RasMol ]
		Tyr A:309 - Pro A:310	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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Description

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Ligands, Modified Residues, Ions (3, 8)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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