2YOB - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   HIGH RESOLUTION AGXT_M STRUCTURE

Authors :   I. Fabelo-Rosa, N. Mesa-Torres, D. Riverol, C. Yunta, A. Albert, E. Sal A. L. Pey

Date :   22 Oct 12 (Deposition) - 30 Oct 13 (Release) - 20 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Transferase, Primary Hyperoxaluria Type I, Agxt Folding And Stability Defects (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Mesa-Torres, I. Fabelo-Rosa, D. Riverol, C. Yunta, A. Albert, E. Salido, A. L. Pey
The Role Of Protein Denaturation Energetics And Molecular Chaperones In The Aggregation And Mistargeting Of Mutants Causing Primary Hyperoxaluria Type I
Plos One V. 8 71963 2013
PubMed-ID: 24205397 | Reference-DOI: 10.1371/JOURNAL.PONE.0071963

Molecule 1 - SERINE--PYRUVATE AMINOTRANSFERASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCOLDII
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SPT, ALANINE--GLYOXYLATE AMINOTRANSFERASE, AGT

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 12)

No.	Name	Count	Type	Full Name
1	BTB	2	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	GOL	6	Ligand/Ion	GLYCEROL
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
4	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:81 , GLY A:82 , HIS A:83 , TRP A:108 , GLY A:156 , SER A:158 , ASP A:183 , VAL A:185 , ALA A:186 , GLN A:208 , LYS A:209 , TYR B:260 , THR B:263	BINDING SITE FOR RESIDUE PLP A1389
02	AC2	SOFTWARE	TYR A:260 , THR A:263 , SER B:81 , GLY B:82 , HIS B:83 , TRP B:108 , GLY B:156 , SER B:158 , ASP B:183 , VAL B:185 , ALA B:186 , GLN B:208 , LYS B:209	BINDING SITE FOR RESIDUE PLP B1389
03	AC3	SOFTWARE	ARG B:258 , HOH B:2009 , HOH B:2073 , HOH B:2231 , HOH B:2303 , HOH B:2304	BINDING SITE FOR RESIDUE SO4 B1390
04	AC4	SOFTWARE	TRP A:246 , ASN A:249 , ASP A:254 , MET A:259 , HOH A:2288 , HOH A:2290	BINDING SITE FOR RESIDUE BTB A1390
05	AC5	SOFTWARE	HOH A:2193 , LYS B:245 , TRP B:246 , ASN B:249 , ASP B:254 , GLN B:256 , MET B:259 , GOL B:1393 , HOH B:2221	BINDING SITE FOR RESIDUE BTB B1391
06	AC6	SOFTWARE	LYS A:5 , ARG B:197 , HIS B:342	BINDING SITE FOR RESIDUE SO4 A1391
07	AC7	SOFTWARE	ASN A:72 , SER A:223 , ASP A:224 , HOH A:2145 , HOH A:2260 , HOH A:2272	BINDING SITE FOR RESIDUE GOL A1392
08	AC8	SOFTWARE	SER A:50 , LYS A:51 , HOH A:2109 , HOH A:2111 , HOH A:2389 , HOH A:2390 , GLN B:23 , MET B:340	BINDING SITE FOR RESIDUE GOL A1393
09	AC9	SOFTWARE	MET A:38 , ALA A:39 , GLY A:42 , HOH A:2092 , HOH A:2096 , HOH A:2392 , GLY B:42	BINDING SITE FOR RESIDUE GOL A1394
10	BC1	SOFTWARE	THR B:135 , LEU B:136 , HOH B:2148 , HOH B:2307	BINDING SITE FOR RESIDUE GOL B1392
11	BC2	SOFTWARE	VAL A:336 , SER A:337 , MET A:340 , HOH A:2347 , HOH A:2352 , HOH A:2356 , HOH A:2365 , HOH A:2393	BINDING SITE FOR RESIDUE GOL A1395
12	BC3	SOFTWARE	HOH A:2182 , HOH A:2193 , LYS B:236 , TRP B:246 , BTB B:1391 , HOH B:2220	BINDING SITE FOR RESIDUE GOL B1393

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:29	-	Pro A:30
2	Gly B:29	-	Pro B:30

Asymmetric/Biological Unit (49, 98)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_060547	T	9	N	SPYA_HUMAN	Polymorphism	115014558	A/B	T	9	N
02	UniProt	VAR_000587	P	11	L	SPYA_HUMAN	Polymorphism	34116584	A/B	P	11	L
03	UniProt	VAR_048236	N	22	S	SPYA_HUMAN	Polymorphism	34885252	A/B	N	22	S
04	UniProt	VAR_074582	R	36	C	SPYA_HUMAN	Disease (HP1)	180177157	A/B	R	36	C
05	UniProt	VAR_074583	G	41	E	SPYA_HUMAN	Disease (HP1)	180177168	A/B	G	41	E
06	UniProt	VAR_000588	G	41	R	SPYA_HUMAN	Disease (HP1)	121908523	A/B	G	41	R
07	UniProt	VAR_010969	G	41	V	SPYA_HUMAN	Disease (HP1)	180177168	A/B	G	41	V
08	UniProt	VAR_074584	G	47	R	SPYA_HUMAN	Disease (HP1)	180177173	A/B	G	47	R
09	UniProt	VAR_008878	G	82	E	SPYA_HUMAN	Disease (HP1)	121908522	A/B	G	82	E
10	UniProt	VAR_060548	G	82	R	SPYA_HUMAN	Disease (HP1)	180177185	A/B	G	82	R
11	UniProt	VAR_060549	W	108	R	SPYA_HUMAN	Disease (HP1)	180177197	A/B	W	108	R
12	UniProt	VAR_060550	A	112	D	SPYA_HUMAN	Disease (HP1)	796052061	A/B	A	112	D
13	UniProt	VAR_010971	G	116	R	SPYA_HUMAN	Disease (HP1)	180177207	A/B	G	116	R
14	UniProt	VAR_074585	L	150	P	SPYA_HUMAN	Disease (HP1)	180177222	A/B	L	150	P
15	UniProt	VAR_000589	F	152	I	SPYA_HUMAN	Disease (HP1)	121908524	A/B	F	152	I
16	UniProt	VAR_060552	L	153	V	SPYA_HUMAN	Disease (HP1)	180177223	A/B	L	153	V
17	UniProt	VAR_010972	G	156	R	SPYA_HUMAN	Disease (HP1)	121908530	A/B	G	156	R
18	UniProt	VAR_060553	S	158	L	SPYA_HUMAN	Disease (HP1)	180177225	A/B	S	158	L
19	UniProt	VAR_074586	G	161	C	SPYA_HUMAN	Disease (HP1)	180177227	A/B	G	161	C
20	UniProt	VAR_060554	G	161	R	SPYA_HUMAN	Disease (HP1)	180177227	A/B	G	161	R
21	UniProt	VAR_074587	G	161	S	SPYA_HUMAN	Disease (HP1)	180177227	A/B	G	161	S
22	UniProt	VAR_074588	L	166	P	SPYA_HUMAN	Disease (HP1)	180177230	A/B	L	166	P
23	UniProt	VAR_000590	G	170	R	SPYA_HUMAN	Disease (HP1)	121908529	A/B	G	170	R
24	UniProt	VAR_060555	C	173	Y	SPYA_HUMAN	Disease (HP1)	180177231	A/B	C	173	Y
25	UniProt	VAR_010973	D	183	N	SPYA_HUMAN	Disease (HP1)	180177236	A/B	D	183	N
26	UniProt	VAR_000591	S	187	F	SPYA_HUMAN	Disease (HP1)	180177238	A/B	S	187	F
27	UniProt	VAR_060556	G	190	R	SPYA_HUMAN	Disease (HP1)	180177239	A/B	G	190	R
28	UniProt	VAR_060557	M	195	R	SPYA_HUMAN	Disease (HP1)	180177244	A/B	M	195	R
29	UniProt	VAR_060558	D	201	E	SPYA_HUMAN	Disease (HP1)	180177246	A/B	D	201	E
30	UniProt	VAR_074589	I	202	N	SPYA_HUMAN	Unclassified (HP1)	---	A/B	I	202	N
31	UniProt	VAR_000592	S	205	P	SPYA_HUMAN	Disease (HP1)	121908520	A/B	S	205	P
32	UniProt	VAR_060559	S	218	L	SPYA_HUMAN	Disease (HP1)	180177253	A/B	S	218	L
33	UniProt	VAR_008879	R	233	C	SPYA_HUMAN	Disease (HP1)	121908526	A/B	R	233	C
34	UniProt	VAR_008880	R	233	H	SPYA_HUMAN	Disease (HP1)	121908527	A/B	R	233	H
35	UniProt	VAR_060560	R	233	L	SPYA_HUMAN	Disease (HP1)	121908527	A/B	R	233	L
36	UniProt	VAR_060561	D	243	H	SPYA_HUMAN	Disease (HP1)	180177258	A/B	D	243	H
37	UniProt	VAR_008881	I	244	T	SPYA_HUMAN	Disease (HP1)	121908525	A/B	I	244	T
38	UniProt	VAR_060562	C	253	R	SPYA_HUMAN	Disease (HP1)	180177264	A/B	C	253	R
39	UniProt	VAR_060563	I	279	M	SPYA_HUMAN	Disease (HP1)	180177277	A/B	I	279	M
40	UniProt	VAR_060564	I	279	T	SPYA_HUMAN	Polymorphism	140992177	A/B	I	279	T
41	UniProt	VAR_060565	A	280	V	SPYA_HUMAN	Polymorphism	73106685	A/B	A	280	V
42	UniProt	VAR_060566	S	287	T	SPYA_HUMAN	Disease (HP1)	180177289	A/B	S	287	T
43	UniProt	VAR_060567	R	289	C	SPYA_HUMAN	Disease (HP1)	180177290	A/B	R	289	C
44	UniProt	VAR_048237	A	295	T	SPYA_HUMAN	Polymorphism	13408961	A/B	A	295	T
45	UniProt	VAR_060569	L	298	P	SPYA_HUMAN	Disease (HP1)	180177293	A/B	L	298	P
46	UniProt	VAR_060570	V	326	I	SPYA_HUMAN	Polymorphism	115057148	A/B	V	326	I
47	UniProt	VAR_060571	V	336	D	SPYA_HUMAN	Disease (HP1)	180177155	A/B	V	336	D
48	UniProt	VAR_000593	I	340	M	SPYA_HUMAN	Polymorphism	4426527	A/B	M	340	M
49	UniProt	VAR_060572	G	350	D	SPYA_HUMAN	Disease (HP1)	180177156	A/B	G	350	D

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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.	SPYA_HUMAN	200-220	2	A:200-220 B:200-220

Asymmetric/Biological Unit (11, 22)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000307503	1a	ENSE00001843474	chr2:241807896-241808447	552	SPYA_HUMAN	1-55	55	2	A:4-55 B:4-55	52 52
1.2	ENST00000307503	2	ENSE00001162366	chr2:241808587-241808779	193	SPYA_HUMAN	56-120	65	2	A:56-120 B:56-120	65 65
1.3	ENST00000307503	3	ENSE00001162358	chr2:241810061-241810125	65	SPYA_HUMAN	120-141	22	2	A:120-141 B:120-141	22 22
1.4b	ENST00000307503	4b	ENSE00001162348	chr2:241810766-241810866	101	SPYA_HUMAN	142-175	34	2	A:142-175 B:142-175	34 34
1.5a	ENST00000307503	5a	ENSE00001162341	chr2:241812396-241812466	71	SPYA_HUMAN	175-199	25	2	A:175-199 B:175-199	25 25
1.6	ENST00000307503	6	ENSE00001162333	chr2:241813395-241813479	85	SPYA_HUMAN	199-227	29	2	A:199-227 B:199-227	29 29
1.7	ENST00000307503	7	ENSE00001162328	chr2:241814526-241814621	96	SPYA_HUMAN	227-259	33	2	A:227-259 B:227-259	33 33
1.8a	ENST00000307503	8a	ENSE00001162322	chr2:241815352-241815421	70	SPYA_HUMAN	259-282	24	2	A:259-282 B:259-282	24 24
1.9b	ENST00000307503	9b	ENSE00001162318	chr2:241816954-241817049	96	SPYA_HUMAN	283-314	32	2	A:283-314 B:283-314	32 32
1.10	ENST00000307503	10	ENSE00001162312	chr2:241817439-241817567	129	SPYA_HUMAN	315-357	43	2	A:315-357 B:315-357	43 43
1.11a	ENST00000307503	11a	ENSE00001895938	chr2:241818131-241818537	407	SPYA_HUMAN	358-392	35	2	A:358-388 B:358-388	31 31

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:385
 aligned with SPYA_HUMAN | P21549 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:385
                                    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       363       373       383     
           SPYA_HUMAN     4 HKLLVTPPKALLKPLSIPNQLLLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLVISGSGHCALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPMTKDPGGHYTLQEVEEGLAQHKPVLLFLTHGESSTGVLQPLDGFGELCHRYKCLLLVDSVASLGGTPLYMDRQGIDILYSGSQKALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIKWLANFWGCDDQPRMYHHTIPVISLYSLRESLALIAEQGLENSWRQHREAAAYLHGRLQALGLQLFVKDPALRLPTVTTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPSTGKVLRIGLLGCNATRENVDRVTEALRAALQHCP 388
               SCOP domains d2yoba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh.......ee........hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhh..eeeee.ee....ee....hhhhhhhhh..eeeee..................eeeee...........eeeeehhhhhhhhh...........hhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhh....eeeee.....hhhhhhhhhhhhhhee....hhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) -----N-L----------S-------------C----E-----R----------------------------------E-------------------------R---D---R---------------------------------P-IV--R-L--C----P---R--Y---------N---F--R----R-----EN--P------------L--------------C---------HT--------R-------------------------MV------T-C-----T--P---------------------------I---------D---M---------D-------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------R----------------------------------------R------------------------------------------------------------------------------R-----------------------------------------------------------------------H---------------------------------------------T------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -------------------------------------V-----------------------------------------------------------------------------------------------------------------------S-----------------------------------------------------------------------L----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:4-55 UniProt: 1-55 [INCOMPLETE]   Exon 1.2  PDB: A:56-120 UniProt: 56-120                          ---------------------Exon 1.4b  PDB: A:142-175         -----------------------Exon 1.6  PDB: A:199-227     -------------------------------Exon 1.8a  PDB: A:259-28Exon 1.9b  PDB: A:283-314       Exon 1.10  PDB: A:315-357 UniProt: 315-357 Exon 1.11a  PDB: A:358-388      Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------Exon 1.3              ---------------------------------Exon 1.5a  PDB: A:175-199---------------------------Exon 1.7  PDB: A:227-259         --------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2yob A   4 HKLLVTPPKALLKPLSIPNQLLLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLVISGSGHCALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPMTKDPGGHYTLQEVEEGLAQHKPVLLFLTHGESSTGVLQPLDGFGELCHRYKCLLLVDSVASLGGTPLYMDRQGIDILYSGSQKALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIKWLANFWGCDDQPRMYHHTIPVISLYSLRESLALIAEQGLENSWRQHREAAAYLHGRLQALGLQLFVKDPALRLPTVTTVAVPAGYDWRDIVSYVMDHFDIEIMGGLGPSTGKVLRIGLLGCNATRENVDRVTEALRAALVAQA 388
                                    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       363       373       383

Chain B from PDB  Type:PROTEIN  Length:385
 aligned with SPYA_HUMAN | P21549 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:385
                                    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       363       373       383     
           SPYA_HUMAN     4 HKLLVTPPKALLKPLSIPNQLLLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLVISGSGHCALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPMTKDPGGHYTLQEVEEGLAQHKPVLLFLTHGESSTGVLQPLDGFGELCHRYKCLLLVDSVASLGGTPLYMDRQGIDILYSGSQKALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIKWLANFWGCDDQPRMYHHTIPVISLYSLRESLALIAEQGLENSWRQHREAAAYLHGRLQALGLQLFVKDPALRLPTVTTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPSTGKVLRIGLLGCNATRENVDRVTEALRAALQHCP 388
               SCOP domains d2yobb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh.......ee........hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhh..eeeee.ee....ee....hhhhhhhhh..eeeee..................eeeee...........eeeeehhhhhhhhh...........hhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhh....eeeee.....hhhhhhhhhhhhhhee....hhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) -----N-L----------S-------------C----E-----R----------------------------------E-------------------------R---D---R---------------------------------P-IV--R-L--C----P---R--Y---------N---F--R----R-----EN--P------------L--------------C---------HT--------R-------------------------MV------T-C-----T--P---------------------------I---------D---M---------D-------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------R----------------------------------------R------------------------------------------------------------------------------R-----------------------------------------------------------------------H---------------------------------------------T------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -------------------------------------V-----------------------------------------------------------------------------------------------------------------------S-----------------------------------------------------------------------L----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:4-55 UniProt: 1-55 [INCOMPLETE]   Exon 1.2  PDB: B:56-120 UniProt: 56-120                          ---------------------Exon 1.4b  PDB: B:142-175         -----------------------Exon 1.6  PDB: B:199-227     -------------------------------Exon 1.8a  PDB: B:259-28Exon 1.9b  PDB: B:283-314       Exon 1.10  PDB: B:315-357 UniProt: 315-357 Exon 1.11a  PDB: B:358-388      Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------Exon 1.3              ---------------------------------Exon 1.5a  PDB: B:175-199---------------------------Exon 1.7  PDB: B:227-259         --------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2yob B   4 HKLLVTPPKALLKPLSIPNQLLLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQIMDEIKEGIQYVFQTRNPLTLVISGSGHCALEAALVNVLEPGDSFLVGANGIWGQRAVDIGERIGARVHPMTKDPGGHYTLQEVEEGLAQHKPVLLFLTHGESSTGVLQPLDGFGELCHRYKCLLLVDSVASLGGTPLYMDRQGIDILYSGSQKALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIKWLANFWGCDDQPRMYHHTIPVISLYSLRESLALIAEQGLENSWRQHREAAAYLHGRLQALGLQLFVKDPALRLPTVTTVAVPAGYDWRDIVSYVMDHFDIEIMGGLGPSTGKVLRIGLLGCNATRENVDRVTEALRAALVAQA 388
                                    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       363       373       383

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: Cystathionine synthase-like (64)

Protein domain: automated matches (14)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d2yoba_	A:
1b	d2yobb_	B:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SPYA_HUMAN | P21549)

molecular function
	GO:0008453	alanine-glyoxylate transaminase activity	Catalysis of the reaction: L-alanine + glyoxylate = pyruvate + glycine.
	GO:0016597	amino acid binding	Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0043621	protein self-association	Interacting selectively and non-covalently with a domain within the same polypeptide.
	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:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0004760	serine-pyruvate transaminase activity	Catalysis of the reaction: L-serine + pyruvate = 3-hydroxypyruvate + L-alanine.
	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:0042853	L-alanine catabolic process	The chemical reactions and pathways resulting in the breakdown of L-alanine, the L-enantiomer of 2-aminopropanoic acid, i.e. (2S)-2-aminopropanoic acid.
	GO:0019448	L-cysteine catabolic process	The chemical reactions and pathways resulting in the breakdown of L-cysteine, the L-enantiomer of 2-amino-3-mercaptopropanoic acid, i.e. (2R)-2-amino-3-mercaptopropanoic acid.
	GO:0007219	Notch signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	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.
	GO:0009436	glyoxylate catabolic process	The chemical reactions and pathways resulting in the breakdown of glyoxylate, the anion of glyoxylic acid, HOC-COOH.
	GO:0046487	glyoxylate metabolic process	The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH.
	GO:0046724	oxalic acid secretion	The controlled release of oxalic acid, ethanedioic acid, by a cell or a tissue.
	GO:0010498	proteasomal protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome.
	GO:0042866	pyruvate biosynthetic process	The chemical reactions and pathways resulting in the formation of pyruvate, 2-oxopropanoate.
	GO:0051591	response to cAMP	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
	GO:0051384	response to glucocorticoid	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
cellular component
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005782	peroxisomal matrix	The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
	GO:0005777	peroxisome	A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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	2yob
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	SPYA_HUMAN \| P21549	:	1h0c 1j04 3r9a 4cbr 4cbs 4i8a 4kxk 4kyo 5f9s 5hhy

1h0c	THE CRYSTAL STRUCTURE OF HUMAN ALANINE:GLYOXYLATE AMINTRANSFERASE.
1j04	STRUCTURAL MECHANISM OF ENZYME MISTARGETING IN HEREDITARYKIDNEY STONE DISEASE IN VITRO

Description

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Ligands, Modified Residues, Ions (4, 12)

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