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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF HUMAN CYSTATHIONASE (CYSTATHIONINE GAMMA LYASE) IN COMPLEX WITH DL-PROPARGYLGLYCINE

Authors :   R. Collins, T. Karlberg, L. Lehtio, C. H. Arrowsmith, H. Berglund, L. G. A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Jo A. Kallas, T. Kotenyova, M. Moche, M. E. Nilsson, P. Nordlund, T. Nyman K. Olesen, C. Persson, H. Schuler, L. Svensson, A. G. Thorsell, L. Tres S. Van Den Berg, J. Sagermark, R. D. Busam, M. Welin, J. Weigelt, M. Wi Structural Genomics Consortium (Sgc)

Date :   28 Mar 08 (Deposition) - 27 May 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Cth, Plp, Propargylglycine, Sgc, Inhibitor, Structural Genomics, Sgc Stockholm, Structural Genomics Consortium, Amino-Acid Biosynthesis, Cysteine Biosynthesis, Disease Mutation, Lyase, Phosphoprotein, Pyridoxal Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Sun, R. Collins, S. Huang, L. Holmberg-Schiavone, G. S. Anand, C. H. Tan, S. Van-Den-Berg, L. W. Deng, P. K. Moore, T. Karlberg, J. Sivaraman
Structural Basis For The Inhibition Mechanism Of Human Cystathionine Gamma-Lyase, An Enzyme Responsible For The Production Of H(2)S.
J. Biol. Chem. V. 284 3076 2009
PubMed-ID: 19019829 | Reference-DOI: 10.1074/JBC.M805459200

Molecule 1 - CYSTATHIONINE GAMMA-LYASE
	Chains	:	A, B, C, D
	EC Number	:	4.4.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Vector Type	:	PLASMID
	Gene	:	CTH
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Synonym	:	GAMMA-CYSTATHIONASE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 15)

No.	Name	Count	Type	Full Name
1	2AG	3	Ligand/Ion	(2S)-2-AMINOPENT-4-ENOIC ACID
2	GOL	5	Ligand/Ion	GLYCEROL
3	NO3	3	Ligand/Ion	NITRATE ION
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PLP	3	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR C:114 , ASN C:161 , LYS C:212 , SER C:340 , LEU C:341 , THR C:355 , ARG C:375	BINDING SITE FOR RESIDUE NO3 C 606
02	AC2	SOFTWARE	TYR D:114 , ASN D:161 , LYS D:212 , SER D:340 , LEU D:341 , THR D:355 , ARG D:375	BINDING SITE FOR RESIDUE NO3 D 607
03	AC3	SOFTWARE	TYR A:114 , ASN A:161 , LYS A:212 , SER A:340 , LEU A:341 , THR A:355 , ARG A:375	BINDING SITE FOR RESIDUE NO3 A 608
04	AC4	SOFTWARE	SER A:89 , GLY A:90 , LEU A:91 , TYR A:114 , ASN A:161 , ASP A:187 , THR A:189 , SER A:209 , THR A:211 , LYS A:212 , TYR B:60 , ARG B:62	BINDING SITE FOR RESIDUE PLP A 500
05	AC5	SOFTWARE	SER C:89 , GLY C:90 , LEU C:91 , TYR C:114 , ASN C:161 , ASP C:187 , THR C:189 , SER C:209 , THR C:211 , LYS C:212 , TYR D:60 , ARG D:62	BINDING SITE FOR RESIDUE PLP C 500
06	AC6	SOFTWARE	TYR C:60 , ARG C:62 , SER D:89 , GLY D:90 , LEU D:91 , TYR D:114 , ASN D:161 , ASP D:187 , SER D:209 , THR D:211 , LYS D:212 , LEU D:341	BINDING SITE FOR RESIDUE PLP D 500
07	AC7	SOFTWARE	TYR A:114 , ARG A:119 , GLU A:339 , TYR B:60 , ARG B:62	BINDING SITE FOR RESIDUE 2AG A 501
08	AC8	SOFTWARE	TYR C:114 , ARG C:119 , GLU C:339 , TYR D:60 , ARG D:62	BINDING SITE FOR RESIDUE 2AG C 501
09	AC9	SOFTWARE	GLU C:59 , TYR C:60 , ARG C:62 , TYR D:114 , ARG D:119 , GLU D:339	BINDING SITE FOR RESIDUE 2AG D 501
10	BC1	SOFTWARE	GLU C:127 , HIS D:99 , LEU D:100 , LEU D:101	BINDING SITE FOR RESIDUE GOL D 601
11	BC2	SOFTWARE	HIS C:99 , LEU C:100 , LEU C:101 , GLU D:127	BINDING SITE FOR RESIDUE GOL C 602
12	BC3	SOFTWARE	HIS A:99 , LEU A:100 , LEU A:101 , GLU B:127	BINDING SITE FOR RESIDUE GOL A 603
13	BC4	SOFTWARE	TRP B:32 , THR B:33 , SER B:34 , TRP D:32 , THR D:33 , SER D:34	BINDING SITE FOR RESIDUE GOL D 604
14	BC5	SOFTWARE	LEU C:43 , SER C:248 , PRO C:249 , ASP D:219 , ASP D:251	BINDING SITE FOR RESIDUE GOL D 605
15	BC6	SOFTWARE	PRO A:295 , HIS A:297 , PRO A:298 , GLN A:299 , HIS A:300 , GLU A:301 , LEU A:302 , ARG A:305	BINDING SITE FOR RESIDUE PEG A 609

(no "SS Bond" information available for 3COG)

Asymmetric/Biological Unit

No.	Residues
1	Thr A:158	-	Pro A:159
2	Asn A:161	-	Pro A:162
3	Thr B:158	-	Pro B:159
4	Asn B:161	-	Pro B:162
5	Thr C:158	-	Pro C:159
6	Asn C:161	-	Pro C:162
7	Thr D:158	-	Pro D:159
8	Asn D:161	-	Pro D:162

Asymmetric/Biological Unit (2, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_015450	T	67	I	CGL_HUMAN	Disease (CSTNU)	28941785	A/B/C/D	T	67	I
2	UniProt	VAR_015451	Q	240	E	CGL_HUMAN	Disease (CSTNU)	28941786	A/B/C/D	Q	240	E

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYS_MET_METAB_PP	PS00868	Cys/Met metabolism enzymes pyridoxal-phosphate attachment site.	CGL_HUMAN	204-218	4	A:204-218 B:204-218 C:204-218 D:204-218

Asymmetric/Biological Unit (12, 48)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000370938	1a	ENSE00002195861	chr1:70876955-70877266	312	CGL_HUMAN	1-56	56	4	A:10-49 B:10-56 C:10-54 D:10-56	40 47 45 47
1.2	ENST00000370938	2	ENSE00000798480	chr1:70881639-70881720	82	CGL_HUMAN	57-84	28	4	A:64-84 B:57-84 C:57-84 D:57-84	21 28 28 28
1.3	ENST00000370938	3	ENSE00000798481	chr1:70883620-70883715	96	CGL_HUMAN	84-116	33	4	A:84-116 B:84-116 C:84-116 D:84-116	33 33 33 33
1.4	ENST00000370938	4	ENSE00000774659	chr1:70887249-70887358	110	CGL_HUMAN	116-152	37	4	A:116-152 B:116-152 C:116-152 D:116-152	37 37 37 37
1.5	ENST00000370938	5	ENSE00000774657	chr1:70889968-70890099	132	CGL_HUMAN	153-196	44	4	A:153-196 B:153-196 C:153-196 D:153-196	44 44 44 44
1.6	ENST00000370938	6	ENSE00000798483	chr1:70895477-70895534	58	CGL_HUMAN	197-216	20	4	A:197-216 B:197-216 C:197-216 D:197-216	20 20 20 20
1.7	ENST00000370938	7	ENSE00000798484	chr1:70896000-70896077	78	CGL_HUMAN	216-242	27	4	A:216-242 B:216-242 C:216-242 D:216-242	27 27 27 27
1.8	ENST00000370938	8	ENSE00000798485	chr1:70897766-70897918	153	CGL_HUMAN	242-293	52	4	A:242-293 B:242-293 C:242-293 D:242-293	52 52 52 52
1.9	ENST00000370938	9	ENSE00000774649	chr1:70899511-70899632	122	CGL_HUMAN	293-333	41	4	A:293-333 B:293-333 C:293-333 D:293-333	41 41 41 41
1.10b	ENST00000370938	10b	ENSE00000774647	chr1:70900808-70900860	53	CGL_HUMAN	334-351	18	4	A:334-351 B:334-351 C:334-351 D:334-351	18 18 18 18
1.11	ENST00000370938	11	ENSE00000774646	chr1:70904371-70904509	139	CGL_HUMAN	351-397	47	4	A:351-397 B:351-397 (gaps) C:351-397 D:351-397	47 47 47 47
1.12d	ENST00000370938	12d	ENSE00001829292	chr1:70904784-70905253	470	CGL_HUMAN	398-405	8	4	A:398-399 B:398-400 C:398-401 D:398-401	2 3 4 4

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:376
 aligned with CGL_HUMAN | P32929 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:390
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399
            CGL_HUMAN    10 GFLPHFQHFATQAIHVGQDPEQWTSRAVVPPISLSTTFKQGAPGQHSGFEYSRSGNPTRNCLEKAVAALDGAKYCLAFASGLAATVTITHLLKAGDQIICMDDVYGGTNRYFRQVASEFGLKISFVDCSKIKLLEAAITPETKLVWIETPTNPTQKVIDIEGCAHIVHKHGDIILVVDNTFMSPYFQRPLALGADISMYSATKYMNGHSDVVMGLVSVNCESLHNRLRFLQNSLGAVPSPIDCYLCNRGLKTLHVRMEKHFKNGMAVAQFLESNPWVEKVIYPGLPSHPQHELVKRQCTGCTGMVTFYIKGTLQHAEIFLKNLKLFTLAESLGGFESLAELPAIMTHASVLKNDRDVLGISDTLIRLSVGLEDEEDLLEDLDQALKAAHP 399
               SCOP domains d3coga_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------3cogA01 A:16-262 Type I PLP-depend              ent aspartate aminotransferase-like (Major domain)                                                                                                                                                     3cogA02 A:263-399 Aspartate Aminotransferase, domain 1                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhh.................--------------.hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhh.....eeeee.................eeeee.............eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee..hhhhhhhhhhhh...ee.........eee..........hhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------I----------------------------------------------------------------------------------------------------------------------------------------------------------------------------E--------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:10-49 UniProt: 1-56          Exon 1.2  PDB: A:64-84      -------------------------------Exon 1.4  PDB: A:116-152             Exon 1.5  PDB: A:153-196 UniProt: 153-196   Exon 1.6            -------------------------Exon 1.8  PDB: A:242-293 UniProt: 242-293           ----------------------------------------Exon 1.10b        ----------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------Exon 1.3  PDB: A:84-116          ---------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:216-242   --------------------------------------------------Exon 1.9  PDB: A:293-333 UniProt: 293-333-----------------Exon 1.11  PDB: A:351-397 UniProt: 351-397     -- Transcript 1 (2)
                 3cog A  10 GFLPHFQHFATQAIHVGQDPEQWTSRAVVPPISLSTTFKQ--------------GNPTRNCLEKAVAALDGAKYCLAFASGLAATVTITHLLKAGDQIICMDDVYGGTNRYFRQVASEFGLKISFVDCSKIKLLEAAITPETKLVWIETPTNPTQKVIDIEGCAHIVHKHGDIILVVDNTFMSPYFQRPLALGADISMYSATKYMNGHSDVVMGLVSVNCESLHNRLRFLQNSLGAVPSPIDCYLCNRGLKTLHVRMEKHFKNGMAVAQFLESNPWVEKVIYPGLPSHPQHELVKRQCTGCTGMVTFYIKGTLQHAEIFLKNLKLFTLAESLGGFESLAELPAIMTHASVLKNDRDVLGISDTLIRLSVGLEDEEDLLEDLDQALKAAHP 399
                                    19        29        39        49         -    |   69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399
                                                                  49             64

Chain B from PDB  Type:PROTEIN  Length:373
 aligned with CGL_HUMAN | P32929 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:391
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399 
            CGL_HUMAN    10 GFLPHFQHFATQAIHVGQDPEQWTSRAVVPPISLSTTFKQGAPGQHSGFEYSRSGNPTRNCLEKAVAALDGAKYCLAFASGLAATVTITHLLKAGDQIICMDDVYGGTNRYFRQVASEFGLKISFVDCSKIKLLEAAITPETKLVWIETPTNPTQKVIDIEGCAHIVHKHGDIILVVDNTFMSPYFQRPLALGADISMYSATKYMNGHSDVVMGLVSVNCESLHNRLRFLQNSLGAVPSPIDCYLCNRGLKTLHVRMEKHFKNGMAVAQFLESNPWVEKVIYPGLPSHPQHELVKRQCTGCTGMVTFYIKGTLQHAEIFLKNLKLFTLAESLGGFESLAELPAIMTHASVLKNDRDVLGISDTLIRLSVGLEDEEDLLEDLDQALKAAHPP 400
               SCOP domains d3cogb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------3cogB01 B:16-262 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                   3cogB02 B:263-400 Aspartate Aminotransferase, domain 1                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhh................................hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh...eeeee.................eeeee.............eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhh.....eeeeee..hhhhhhhhhhhh...ee.........eee..------------------...eeeee....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------I----------------------------------------------------------------------------------------------------------------------------------------------------------------------------E---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:10-56 UniProt: 1-56          Exon 1.2  PDB: B:57-84      -------------------------------Exon 1.4  PDB: B:116-152             Exon 1.5  PDB: B:153-196 UniProt: 153-196   Exon 1.6            -------------------------Exon 1.8  PDB: B:242-293 UniProt: 242-293           ----------------------------------------Exon 1.10b        ----------------------------------------------1.1 Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------Exon 1.3  PDB: B:84-116          ---------------------------------------------------------------------------------------------------Exon 1.7  PDB: B:216-242   --------------------------------------------------Exon 1.9  PDB: B:293-333 UniProt: 293-333-----------------Exon 1.11  PDB: B:351-397 (gaps)               --- Transcript 1 (2)
                 3cog B  10 GFLPHFQHFATQAIHVGQDPEQWTSRAVVPPISLSTTFKQGAPGQHSGFEYSRSGNPTRNCLEKAVAALDGAKYCLAFASGLAATVTITHLLKAGDQIICMDDVYGGTNRYFRQVASEFGLKISFVDCSKIKLLEAAITPETKLVWIETPTNPTQKVIDIEGCAHIVHKHGDIILVVDNTFMSPYFQRPLALGADISMYSATKYMNGHSDVVMGLVSVNCESLHNRLRFLQNSLGAVPSPIDCYLCNRGLKTLHVRMEKHFKNGMAVAQFLESNPWVEKVIYPGLPSHPQHELVKRQCTGCTGMVTFYIKGTLQHAEIFLKNLKLFTLAESLGGFESLAELP------------------SDTLIRLSVGLEDEEDLLEDLDQALKAAHPP 400
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349 |       -         -|      379       389       399 
                                                                                                                                                                                                                                                                                                                                                                               351                370

Chain C from PDB  Type:PROTEIN  Length:390
 aligned with CGL_HUMAN | P32929 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:392
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399  
            CGL_HUMAN    10 GFLPHFQHFATQAIHVGQDPEQWTSRAVVPPISLSTTFKQGAPGQHSGFEYSRSGNPTRNCLEKAVAALDGAKYCLAFASGLAATVTITHLLKAGDQIICMDDVYGGTNRYFRQVASEFGLKISFVDCSKIKLLEAAITPETKLVWIETPTNPTQKVIDIEGCAHIVHKHGDIILVVDNTFMSPYFQRPLALGADISMYSATKYMNGHSDVVMGLVSVNCESLHNRLRFLQNSLGAVPSPIDCYLCNRGLKTLHVRMEKHFKNGMAVAQFLESNPWVEKVIYPGLPSHPQHELVKRQCTGCTGMVTFYIKGTLQHAEIFLKNLKLFTLAESLGGFESLAELPAIMTHASVLKNDRDVLGISDTLIRLSVGLEDEEDLLEDLDQALKAAHPPS 401
               SCOP domains d3cogc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------3cogC01 C:16-262 Type I PLP-dependent a  spartate aminotransferase-like (Major domain)                                                                                                                                                                 3cogC02 C:263-401 Aspartate Aminotransferase, domain 1                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhh......................--........hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh...eeeee...hhhhhh........eeeee.............eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee..hhhhhhhhhhhh...ee.........eee..........hhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------I----------------------------------------------------------------------------------------------------------------------------------------------------------------------------E----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: C:10-54 UniProt: 1-56          Exon 1.2  PDB: C:57-84      -------------------------------Exon 1.4  PDB: C:116-152             Exon 1.5  PDB: C:153-196 UniProt: 153-196   Exon 1.6            -------------------------Exon 1.8  PDB: C:242-293 UniProt: 242-293           ----------------------------------------Exon 1.10b        ----------------------------------------------1.12 Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------Exon 1.3  PDB: C:84-116          ---------------------------------------------------------------------------------------------------Exon 1.7  PDB: C:216-242   --------------------------------------------------Exon 1.9  PDB: C:293-333 UniProt: 293-333-----------------Exon 1.11  PDB: C:351-397 UniProt: 351-397     ---- Transcript 1 (2)
                 3cog C  10 GFLPHFQHFATQAIHVGQDPEQWTSRAVVPPISLSTTFKQGAPGQ--GFEYSRSGNPTRNCLEKAVAALDGAKYCLAFASGLAATVTITHLLKAGDQIICMDDVYGGTNRYFRQVASEFGLKISFVDCSKIKLLEAAITPETKLVWIETPTNPTQKVIDIEGCAHIVHKHGDIILVVDNTFMSPYFQRPLALGADISMYSATKYMNGHSDVVMGLVSVNCESLHNRLRFLQNSLGAVPSPIDCYLCNRGLKTLHVRMEKHFKNGMAVAQFLESNPWVEKVIYPGLPSHPQHELVKRQCTGCTGMVTFYIKGTLQHAEIFLKNLKLFTLAESLGGFESLAELPAIMTHASVLKNDRDVLGISDTLIRLSVGLEDEEDLLEDLDQALKAAHPPS 401
                                    19        29        39        49    |  |59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399  
                                                                       54 57

Chain D from PDB  Type:PROTEIN  Length:392
 aligned with CGL_HUMAN | P32929 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:392
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399  
            CGL_HUMAN    10 GFLPHFQHFATQAIHVGQDPEQWTSRAVVPPISLSTTFKQGAPGQHSGFEYSRSGNPTRNCLEKAVAALDGAKYCLAFASGLAATVTITHLLKAGDQIICMDDVYGGTNRYFRQVASEFGLKISFVDCSKIKLLEAAITPETKLVWIETPTNPTQKVIDIEGCAHIVHKHGDIILVVDNTFMSPYFQRPLALGADISMYSATKYMNGHSDVVMGLVSVNCESLHNRLRFLQNSLGAVPSPIDCYLCNRGLKTLHVRMEKHFKNGMAVAQFLESNPWVEKVIYPGLPSHPQHELVKRQCTGCTGMVTFYIKGTLQHAEIFLKNLKLFTLAESLGGFESLAELPAIMTHASVLKNDRDVLGISDTLIRLSVGLEDEEDLLEDLDQALKAAHPPS 401
               SCOP domains d3cogd_ D: automated matches                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------3cogD01 D:16-262 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                   3cogD02 D:263-401 Aspartate Aminotransferase, domain 1                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhh................................hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh...eeeee.........hhhhhh..eeeee.............eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee..hhhhhhhhhhhh...ee.........eee..........hhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------I----------------------------------------------------------------------------------------------------------------------------------------------------------------------------E----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: D:10-56 UniProt: 1-56          Exon 1.2  PDB: D:57-84      -------------------------------Exon 1.4  PDB: D:116-152             Exon 1.5  PDB: D:153-196 UniProt: 153-196   Exon 1.6            -------------------------Exon 1.8  PDB: D:242-293 UniProt: 242-293           ----------------------------------------Exon 1.10b        ----------------------------------------------1.12 Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------Exon 1.3  PDB: D:84-116          ---------------------------------------------------------------------------------------------------Exon 1.7  PDB: D:216-242   --------------------------------------------------Exon 1.9  PDB: D:293-333 UniProt: 293-333-----------------Exon 1.11  PDB: D:351-397 UniProt: 351-397     ---- Transcript 1 (2)
                 3cog D  10 GFLPHFQHFATQAIHVGQDPEQWTSRAVVPPISLSTTFKQGAPGQHSGFEYSRSGNPTRNCLEKAVAALDGAKYCLAFASGLAATVTITHLLKAGDQIICMDDVYGGTNRYFRQVASEFGLKISFVDCSKIKLLEAAITPETKLVWIETPTNPTQKVIDIEGCAHIVHKHGDIILVVDNTFMSPYFQRPLALGADISMYSATKYMNGHSDVVMGLVSVNCESLHNRLRFLQNSLGAVPSPIDCYLCNRGLKTLHVRMEKHFKNGMAVAQFLESNPWVEKVIYPGLPSHPQHELVKRQCTGCTGMVTFYIKGTLQHAEIFLKNLKLFTLAESLGGFESLAELPAIMTHASVLKNDRDVLGISDTLIRLSVGLEDEEDLLEDLDQALKAAHPPS 401
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399

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( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: PLP-dependent transferase-like (627)

Superfamily: PLP-dependent transferases (625)

Family: automated matches (163)

Protein domain: automated matches (163)

Human (Homo sapiens) [TaxId: 9606] (17)

1a	d3coga_	A:
1b	d3cogb_	B:
1c	d3cogc_	C:
1d	d3cogd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Aspartate Aminotransferase; domain 2 (384)

Homologous Superfamily: Type I PLP-dependent aspartate aminotransferase-like (Major domain) (384)

Human (Homo sapiens) (18)

1a	3cogB01	B:16-262
1b	3cogD01	D:16-262
1c	3cogC01	C:16-262
1d	3cogA01	A:16-262

Architecture: Alpha-Beta Complex (3881)

Topology: Aspartate Aminotransferase, domain 1 (355)

Homologous Superfamily: Aspartate Aminotransferase, domain 1 (354)

Human (Homo sapiens) (15)

2a	3cogA02	A:263-399
2b	3cogC02	C:263-401
2c	3cogD02	D:263-401
2d	3cogB02	B:263-400

(no "Pfam Domain" information available for 3COG)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (CGL_HUMAN | P32929)

molecular function
	GO:0080146	L-cysteine desulfhydrase activity	Catalysis of the reaction: L-cysteine + H2O = ammonia + pyruvate + hydrogen sulfide + H+.
	GO:0044540	L-cystine L-cysteine-lyase (deaminating)	Catalysis of the reaction: L-cystine + H2O <=> pyruvate + NH3 + thiocysteine. Thiocysteine is also known as cysteine persulfide.
	GO:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
	GO:0016846	carbon-sulfur lyase activity	Catalysis of the elimination of hydrogen sulfide or substituted H2S.
	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:0004123	cystathionine gamma-lyase activity	Catalysis of the reaction: L-cystathionine + H2O = 2-oxobutanoate + L-cysteine + NH4+.
	GO:0047982	homocysteine desulfhydrase activity	Catalysis of the reaction: L-homocysteine + H2O = sulfide + NH3 + 2-oxobutanoate.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	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: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.
biological process
	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:0019344	cysteine biosynthetic process	The chemical reactions and pathways resulting in the formation of cysteine, 2-amino-3-mercaptopropanoic acid.
	GO:0019343	cysteine biosynthetic process via cystathionine	The chemical reactions and pathways resulting in the formation of cysteine, via the intermediate cystathionine.
	GO:0006534	cysteine metabolic process	The chemical reactions and pathways involving cysteine, 2-amino-3-mercaptopropanoic acid.
	GO:0030968	endoplasmic reticulum unfolded protein response	The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation.
	GO:0070814	hydrogen sulfide biosynthetic process	The chemical reactions and pathways resulting in the formation of hydrogen sulfide, H2S.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:2001234	negative regulation of apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway.
	GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
	GO:0051092	positive regulation of NF-kappaB transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
	GO:1904831	positive regulation of aortic smooth muscle cell differentiation	Any process that activates or increases the frequency, rate or extent of aortic smooth muscle cell differentiation.
	GO:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
	GO:0044524	protein sulfhydration	The modification of a protein amino acid by the addition of sulfur.
	GO:0018272	protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine	The modification of peptidyl-lysine to form N6-pyridoxal phosphate-L-lysine.
	GO:0000098	sulfur amino acid catabolic process	The chemical reactions and pathways resulting in the breakdown of amino acids containing sulfur, comprising cysteine, methionine and selenocysteine.
	GO:0019346	transsulfuration	The interconversion of homocysteine and cysteine via cystathionine. In contrast with enteric bacteria and mammals, Saccharomyces cerevisiae has two transsulfuration pathways employing two separate sets of enzymes.
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.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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	CGL_HUMAN \| P32929	:	2nmp 3elp 5eig

2nmp	CRYSTAL STRUCTURE OF HUMAN CYSTATHIONINE GAMMA LYASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 8)

PROSITE Motifs (1, 4)

Exons (12, 48)

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