1G0D - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF RED SEA BREAM TRANSGLUTAMINASE

Authors :   K. Noguchi, K. Ishikawa, K. Yokoyama, T. Ohtsuka, N. Nio, E. Suzuki

Date :   06 Oct 00 (Deposition) - 23 May 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

Keywords :   Tissue Transglutaminase, Acyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Noguchi, K. Ishikawa, K. I. Yokoyama, T. Ohtsuka, N. Nio, E. Suzuki
Crystal Structure Of Red Sea Bream Transglutaminase.
J. Biol. Chem. V. 276 12055 2001
PubMed-ID: 11080504 | Reference-DOI: 10.1074/JBC.M009862200
(for further references see the PDB file header)

Molecule 1 - PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.3.2.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTTNCO
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	RED SEABREAM
	Organism Scientific	:	PAGRUS MAJOR
	Organism Taxid	:	143350
	Tissue	:	LIVER

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:150 , ARG A:291 , TRP A:351 , GLU A:434 , HIS A:439 , HOH A:845 , HOH A:931	BINDING SITE FOR RESIDUE SO4 A 696

(no "SS Bond" information available for 1G0D)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:268	-	Tyr A:269
2	Gly A:369	-	Pro A:370
3	Lys A:384	-	Tyr A:385

(no "SAP(SNP)/Variant" information available for 1G0D)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRANSGLUTAMINASES	PS00547	Transglutaminases active site.	TGM2_PAGMA	270-287	1	A:270-287

(no "Exon" information available for 1G0D)

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:666
 aligned with TGM2_PAGMA | P52181 from UniProtKB/Swiss-Prot  Length:695

    Alignment length:679
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675         
           TGM2_PAGMA     6 GLIVDVNGRSHENNLAHRTREIDRERLIVRRGQPFSITLQCSDSLPPKHHLELVLHLGKRDEVVIKVQKEHGARDKWWFNQQGAQDEILLTLHSPANAVIGHYRLAVLVMSPDGHIVERADKISFHMLFNPWCRDDMVYLPDESKLQEYVMNEDGVIYMGTWDYIRSIPWNYGQFEDYVMDICFEVLDNSPAALKNSEMDIEHRSDPVYVGRTITAMVNSNGDRGVLTGRWEEPYTDGVAPYRWTGSVPILQQWSKAGVRPVKYGQCWVFAAVACTVLRCLGIPTRPITNFASAHDVDGNLSVDFLLNERLESLDSRQRSDSSWNFHCWVESWMSREDLPEGNDGWQVLDPTPQELSDGEFCCGPCPVAAIKEGNLGVKYDAPFVFAEVNADTIYWIVQKDGQRRKITEDHASVGKNISTKSVYGNHREDVTLHYKYPEGSQKEREVYKKAGRRVTEPSNEIAEQGRLQLSIKHAQPVFGTDFDVIVEVKNEGGRDAHAQLTMLAMAVTYNSLRRGECQRKTISVTVPAHKAHKEVMRLHYDDYVRCVSEHHLIRVKALLDAPGENGPIMTVANIPLSTPELLVQVPGKAVVWEPLTAYVSFTNPLPVPLKGGVFTLEGAGLLSATQIHVNGAVAPSGKVSVKLSFSPMRTGVRKLLVDFDSDRLKDVKGVTTVVVHKK 684
               SCOP domains d1g0da1 A:6-140 Transglutaminase N-terminal domain                                                                                     d1g0da4 A:141-461 Transglutaminase catalytic domain                                                                                                                                                                                                                                                                                        d1g0da2 A:472-583 Transglutaminase, two C-terminal domains                                                      d1g0da3 A:584-684 Transglutaminase, two C-terminal domains                                            SCOP domains
               CATH domains 1g0dA01 A:6-142 Immunoglobulins                                                                                                          1g0dA02 A:143-472 Coagulation Factor XIII, subunit A, domain 2                                                                                                                                                                                                                                                                            1g0dA03 A:473-585 Immunoglobulins                                                                                1g0dA04 A:586-682 Immunoglobulins                                                                -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhhhhhh..........eee....eeeeeee........eeeeeeee.....eeeee..........eeeeeee..eeeeeee.......eeeeeeeeee.....eeee...eeeeee.............hhhhhhhhh...eeeeeeee..eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......eee..........hhhhh..hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhh..eeeeeeeeehhhhh...eeeeee................eeeeeeeeeee..........eeeeee............eeeeehhhhhh.......hhhhhhhhhhheeeeeee.....eee.ee.........eee......eeehhhhhh....hhhhhhhhhhhh....----------.eeeeeee........eeeeeeeee.....eeeeeeeeeeee...........eeeeeeee....eeeeeeeehhhhhh.......eeeeeeeee..---..eeeeeeee......eee....ee....eeeeeeee......ee..eeeeee...eeeeeee...ee....eeeeeeee.....eeeeeeeeee......eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSGLUTAMINASES ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g0d A   6 GLIVDVNGRSHENNLAHRTREIDRERLIVRRGQPFSITLQCSDSLPPKHHLELVLHLGKRDEVVIKVQKEHGARDKWWFNQQGAQDEILLTLHSPANAVIGHYRLAVLVMSPDGHIVERADKISFHMLFNPWCRDDMVYLPDESKLQEYVMNEDGVIYMGTWDYIRSIPWNYGQFEDYVMDICFEVLDNSPAALKNSEMDIEHRSDPVYVGRTITAMVNSNGDRGVLTGRWEEPYTDGVAPYRWTGSVPILQQWSKAGVRPVKYGQCWVFAAVACTVLRCLGIPTRPITNFASAHDVDGNLSVDFLLNERLESLDSRQRSDSSWNFHCWVESWMSREDLPEGNDGWQVLDPTPQELSDGEFCCGPCPVAAIKEGNLGVKYDAPFVFAEVNADTIYWIVQKDGQRRKITEDHASVGKNISTKSVYGNHREDVTLHYKYPEGSQKEREVYKKAGRRVT----------RLQLSIKHAQPVFGTDFDVIVEVKNEGGRDAHAQLTMLAMAVTYNSLRRGECQRKTISVTVPAHKAHKEVMRLHYDDYVRCVSEHHLIRVKALLDAP---GPIMTVANIPLSTPELLVQVPGKAVVWEPLTAYVSFTNPLPVPLKGGVFTLEGAGLLSATQIHVNGAVAPSGKVSVKLSFSPMRTGVRKLLVDFDSDRLKDVKGVTTVVVHKK 684
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455     |   -      |475       485       495       505       515       525       535       545       555       565  |   |575       585       595       605       615       625       635       645       655       665       675         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 461        472                                                                                             568 572

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Coagulation Factor XIII; Chain A, domain 2 (19)

Homologous Superfamily: Coagulation Factor XIII, subunit A, domain 2 (19)

Red seabream (Pagrus major) (1)

1g0dA02

A:143-472

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Red seabream (Pagrus major) (1)

2a	1g0dA03	A:473-585
2b	1g0dA04	A:586-682
2c	1g0dA01	A:6-142

(no "Pfam Domain" information available for 1G0D)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TGM2_PAGMA | P52181)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0018149	peptide cross-linking	The formation of a covalent cross-link between or within protein chains.

Asymmetric/Biological Unit
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		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:369 - Pro A:370	[ RasMol ]
		Lys A:268 - Tyr A:269	[ RasMol ]
		Lys A:384 - Tyr A:385	[ RasMol ]

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	1g0d
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Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

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Exons (0, 0)

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