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Asym./Biol. Unit (Jmol Viewer)

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Title :   TRANSGLUTAMINASE 2 IN COMPLEX WITH A NOVEL INHIBITOR

Authors :   I. Lindemann, A. Heine, G. Klebe

Date :   18 May 11 (Deposition) - 06 Jun 12 (Release) - 26 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Transglutaminase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Lindemann, J. Boettcher, K. Oertel, J. Weber, M. Hils, R. Pasternack, A. Heine, G. Klebe
Transglutaminase 2 In Complex With A Novel Inhibitor
To Be Published
PubMed: search

Molecule 1 - PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE 2
	Chains	:	A
	EC Number	:	2.3.2.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 2-687
	Gene	:	TGM2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TISSUE TRANSGLUTAMINASE, TRANSGLUTAMINASE C, TG(C), TGC, TGASE C, TRANSGLUTAMINASE H, TGASE H, TRANSGLUTAMINASE-2, TGASE-2

Molecule 2 - PEPTIDE INHIBITOR
	Chains	:	B
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 8)

No.	Name	Count	Type	Full Name
1	PHQ	1	Mod. Amino Acid	BENZYL CHLOROCARBONATE
2	SO4	6	Ligand/Ion	SULFATE ION
3	XW1	1	Mod. Amino Acid	(2S)-2-AMINO-7-ETHOXY-7-OXOHEPTANOIC ACID

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:202 , ARG A:222	BINDING SITE FOR RESIDUE SO4 A 701
2	AC2	SOFTWARE	LYS A:202 , ARG A:209 , TYR A:219	BINDING SITE FOR RESIDUE SO4 A 702
3	AC3	SOFTWARE	ARG A:80	BINDING SITE FOR RESIDUE SO4 A 703
4	AC4	SOFTWARE	ARG A:80 , ASP A:81 , ALA A:82	BINDING SITE FOR RESIDUE SO4 A 704
5	AC5	SOFTWARE	ARG A:478 , VAL A:479 , GLY A:480 , ARG A:580	BINDING SITE FOR RESIDUE SO4 A 705
6	AC6	SOFTWARE	SER A:68 , GLN A:69 , LYS A:74	BINDING SITE FOR RESIDUE SO4 A 706
7	AC7	SOFTWARE	GLN A:169 , GLY A:170 , CYS A:277 , SER A:303 , MET A:330 , ILE A:331 , TRP A:332 , ASN A:333 , PHE A:334 , HIS A:335 , LEU A:420 , TYR A:516 , ASN A:517 , GLU A:557	BINDING SITE FOR CHAIN B OF PEPTIDE INHIBITOR

(no "SS Bond" information available for 3S3P)

Asymmetric/Biological Unit

No.	Residues
1	Gln A:234	-	Gly A:235
2	Gly A:372	-	Pro A:373
3	Lys A:387	-	Tyr A:388

Asymmetric/Biological Unit (7, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052553	R	76	H	TGM2_HUMAN	Polymorphism	41274720	A	R	76	H
2	UniProt	VAR_055357	R	214	H	TGM2_HUMAN	Polymorphism	45530133	A	R	214	H
3	UniProt	VAR_037998	M	330	R	TGM2_HUMAN	Unclassified	141603506	A	M	330	R
4	UniProt	VAR_037999	I	331	N	TGM2_HUMAN	Unclassified	---	A	I	331	N
5	UniProt	VAR_055359	R	436	W	TGM2_HUMAN	Polymorphism	45629036	A	R	436	W
6	UniProt	VAR_052554	P	536	S	TGM2_HUMAN	Polymorphism	45556333	A	P	536	S
7	UniProt	VAR_036554	G	660	V	TGM2_HUMAN	Unclassified	---	A	G	660	V

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRANSGLUTAMINASES	PS00547	Transglutaminases active site.	TGM2_HUMAN	275-292	1	A:277-292

Asymmetric/Biological Unit (13, 13)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000361475	2a	ENSE00001922845	chr20:36793774-36793591	184	TGM2_HUMAN	1-4	4	1	A:2-4	3
1.3b	ENST00000361475	3b	ENSE00000800527	chr20:36790001-36789822	180	TGM2_HUMAN	4-64	61	1	A:4-64	61
1.4a	ENST00000361475	4a	ENSE00000661931	chr20:36784491-36784249	243	TGM2_HUMAN	64-145	82	1	A:64-145	82
1.5b	ENST00000361475	5b	ENSE00000661930	chr20:36779459-36779341	119	TGM2_HUMAN	145-184	40	1	A:145-184	40
1.6	ENST00000361475	6	ENSE00000800526	chr20:36776491-36776363	129	TGM2_HUMAN	185-227	43	1	A:185-227	43
1.7b	ENST00000361475	7b	ENSE00000800525	chr20:36775296-36775119	178	TGM2_HUMAN	228-287	60	1	A:228-287 (gaps)	60
1.8	ENST00000361475	8	ENSE00000661927	chr20:36770601-36770466	136	TGM2_HUMAN	287-332	46	1	A:287-332 (gaps)	46
1.9	ENST00000361475	9	ENSE00000661926	chr20:36769787-36769684	104	TGM2_HUMAN	332-367	36	1	A:332-361	30
1.10	ENST00000361475	10	ENSE00000661925	chr20:36768056-36767814	243	TGM2_HUMAN	367-448	82	1	A:370-448 (gaps)	79
1.11a	ENST00000361475	11a	ENSE00000661924	chr20:36766787-36766515	273	TGM2_HUMAN	448-539	92	1	A:448-539 (gaps)	92
1.12b	ENST00000361475	12b	ENSE00000661923	chr20:36760902-36760742	161	TGM2_HUMAN	539-592	54	1	A:539-592	54
1.13b	ENST00000361475	13b	ENSE00000661922	chr20:36759631-36759495	137	TGM2_HUMAN	593-638	46	1	A:593-638 (gaps)	46
1.14a	ENST00000361475	14a	ENSE00001904837	chr20:36758771-36756863	1909	TGM2_HUMAN	638-687	50	1	A:638-683	46

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:611
 aligned with TGM2_HUMAN | P21980 from UniProtKB/Swiss-Prot  Length:687

    Alignment length:682
                                    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       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681  
           TGM2_HUMAN     2 AEELVLERCDLELETNGRDHHTADLCREKLVVRRGQPFWLTLHFEGRNYEASVDSLTFSVVTGPAPSQEAGTKARFPLRDAVEEGDWTATVVDQQDCTLSLQLTTPANAPIGLYRLSLEASTGYQGSSFVLGHFILLFNAWCPADAVYLDSEEERQEYVLTQQGFIYQGSAKFIKNIPWNFGQFEDGILDICLILLDVNPKFLKNAGRDCSRRSSPVYVGRVVSGMVNCNDDQGVLLGRWDNNYGDGVSPMSWIGSVDILRRWKNHGCQRVKYGQCWVFAAVACTVLRCLGIPTRVVTNYNSAHDQNSNLLIEYFRNEFGEIQGDKSEMIWNFHCWVESWMTRPDLQPGYEGWQALDPTPQEKSEGTYCCGPVPVRAIKEGDLSTKYDAPFVFAEVNADVVDWIQQDDGSVHKSINRSLIVGLKISTKSVGRDEREDITHTYKYPEGSSEEREAFTRANHLNKLAEKEETGMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTVSYNGILGPECGTKYLLNLNLEPFSEKSVPLCILYEKYRDCLTESNLIKVRALLVEPVINSYLLAERDLYLENPEIKIRILGEPKQKRKLVAEVSLQNPLPVALEGCTFTVEGAGLTEEQKTVEIPDPVEAGEEVKVRMDLLPLHMGLHKLVVNFESDKLKAVKGFRNVI 683
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.hhhhhhhhh.hhhhh...eeee....eeeeeee..........eeeeeeee..........eeeee..........eeeeeee...eeeeeee.......eeeeeeeeee....eeeeeeeeeeee.............hhhhhhhhh...eeeeeee....eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.............-------------....hhhhhhhhhh----------hhhhhhhhhhhhhhhh..eeeeeeeee.----.hhhhhhhh----------......eeeeeeeee..........eeeee....--------....eehhhhhh.......hhhhhhhhhh.eeeee..-------.ee....eeeeeeeee......eeehhhhhh....hhhhhhhhhhhhh----------.eeeeee..........eeeeeeeee.....eeeeeeeeeeee.....eeeeeeeeeeeeeee...eeeeeeeeehhhhhh.......eeeeeeeeee....eeeeeeeeee......eee..---------.eeeeee.........eeeeee..........eee........eeeeee.........eeeeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------H-----------------------------------------------------------------------------------------------------------------------------------------H-------------------------------------------------------------------------------------------------------------------RN--------------------------------------------------------------------------------------------------------W---------------------------------------------------------------------------------------------------S---------------------------------------------------------------------------------------------------------------------------V----------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSGLUTAMINASES ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.2-----------------------------------------------------------Exon 1.4a  PDB: A:64-145 UniProt: 64-145                                          ---------------------------------------Exon 1.6  PDB: A:185-227 UniProt: 185-227  Exon 1.7b  PDB: A:228-287 (gaps) UniProt: 228-287           -------------------------------------------------------------------------------Exon 1.10  PDB: A:370-448 (gaps) UniProt: 367-448 [INCOMPLETE]                    ------------------------------------------------------------------------------------------Exon 1.12b  PDB: A:539-592 UniProt: 539-592           Exon 1.13b  PDB: A:593-638 (gaps)             --------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.3b  PDB: A:4-64 UniProt: 4-64                         --------------------------------------------------------------------------------Exon 1.5b  PDB: A:145-184               ------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:287-332 (gaps)               -------------------------------------------------------------------------------------------------------------------Exon 1.11a  PDB: A:448-539 (gaps) UniProt: 448-539                                          --------------------------------------------------------------------------------------------------Exon 1.14a  PDB: A:638-683 UniProt: 638-687    Transcript 1 (2)
           Transcript 1 (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:332-361            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 3s3p A   2 AEELVLERCDLELETNGRDHHTADLCREKLVVRRGQPFWLTLHFEGRNYEASVDSLTFSVVTGPAPSQEAGTKARFPLRDAVEEGDWTATVVDQQDCTLSLQLTTPANAPIGLYRLSLEASTGYQGSSFVLGHFILLFNAWCPADAVYLDSEEERQEYVLTQQGFIYQGSAKFIKNIPWNFGQFEDGILDICLILLDVNPKFLKNAGRDCSRRSSPVYVGRVVSGMVNCNDDQGVLLG-------------SWIGSVDILRRWKN----------CWVFAAVACTVLRCLGIPTRVVTNYNSA----SNLLIEYFR----------SEMIWNFHCWVESWMTRPDLQPGYEGWQALDPTP--------CCGPVPVRAIKEGDLSTKYDAPFVFAEVNADVVDWIQ-------KSINRSLIVGLKISTKSVGRDEREDITHTYKYPEGSSEEREAFTRANH----------GMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTVSYNGILGPECGTKYLLNLNLEPFSEKSVPLCILYEKYRDCLTESNLIKVRALLVEPVINSYLLAERDLYLENPEIKIRIL---------VAEVSLQNPLPVALEGCTFTVEGAGLTEEQKTVEIPDPVEAGEEVKVRMDLLPLHMGLHKLVVNFESDKLKAVKGFRNVI 683
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       | -         - |     261    |    -     | 281       291       301  |    311     |   -      |331       341       351       361       371       381       391       401    |    -  |    421       431       441       451       461         -|      481       491       501       511       521       531       541       551       561       571       581       591  |      -  |    611       621       631       641       651       661       671       681  
                                                                                                                                                                                                                                                                       239           253          266        277                        304  309     317        328                              361      370                                 406     414                                            461        472                                                                                                                       594       604

Chain B from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 3s3p B   1 xaQPL   5
                            ||   
                            1-PHQ
                             2-XW1

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 '\|'

(no "SCOP Domain" information available for 3S3P)

(no "CATH Domain" information available for 3S3P)

(no "Pfam Domain" information available for 3S3P)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TGM2_HUMAN | P21980)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0003810	protein-glutamine gamma-glutamyltransferase activity	Catalysis of the reaction: protein glutamine + alkylamine = protein N5-alkylglutamine + NH3. This reaction is the formation of the N6-(L-isoglutamyl)-L-lysine isopeptide, resulting in cross-linking polypeptide chains; the gamma-carboxamide groups of peptidyl-glutamine residues act as acyl donors, and the 6-amino-groups of peptidyl-lysine residues act as acceptors, to give intra- and intermolecular N6-(5-glutamyl)lysine cross-links.
	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.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0043277	apoptotic cell clearance	The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.
	GO:0060445	branching involved in salivary gland morphogenesis	The process in which the branching structure of the salivary gland is generated and organized.
	GO:0032471	negative regulation of endoplasmic reticulum calcium ion concentration	Any process that decreases the concentration of calcium ions in the endoplasmic reticulum.
	GO:0018149	peptide cross-linking	The formation of a covalent cross-link between or within protein chains.
	GO:0007200	phospholipase C-activating G-protein coupled receptor signaling pathway	The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds with activation of phospholipase C (PLC) and a subsequent increase in the concentration of inositol trisphosphate (IP3) and diacylglycerol (DAG).
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0045785	positive regulation of cell adhesion	Any process that activates or increases the frequency, rate or extent of cell adhesion.
	GO:0051561	positive regulation of mitochondrial calcium ion concentration	Any process that increases the concentration of calcium ions in mitochondria.
	GO:0060662	salivary gland cavitation	The process in which the solid core of salivary epithelium gives rise to the hollow tube of the gland.
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:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	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:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0031226	intrinsic component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gln A:234 - Gly A:235	[ RasMol ]
		Gly A:372 - Pro A:373	[ RasMol ]
		Lys A:387 - Tyr A:388	[ RasMol ]

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	3s3p
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	TGM2_HUMAN \| P21980	:	1fau 1kv3 2q3z 3ly6 3s3j 3s3s 4pyg

Description

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Ligands, Modified Residues, Ions (3, 8)

Sites (7, 7)

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Cis Peptide Bonds (3, 3)

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