1MZA - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN PRO-GRANZYME K

Authors :   C. Hink-Schauer, E. Estebanez-Perpina, E. Wilharm, P. Fuentes- Prior, W. Klinkert, W. Bode, D. E. Jenne

Date :   07 Oct 02 (Deposition) - 14 Jan 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.23

Chains :   Asym./Biol. Unit : A

Keywords :   Granzyme, Apoptosis, Serine Protease, S1 Family, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Hink-Schauer, E. Estebanez-Perpina, E. Wilharm, P. Fuentes-Prior, W. Klinkert, W. Bode, D. E. Jenne
The 2. 2-A Crystal Structure Of Human Pro-Granzyme K Reveals A Rigid Zymogen With Unusual Features
J. Biol. Chem. V. 277 50923 2002
PubMed-ID: 12384499 | Reference-DOI: 10.1074/JBC.M207962200
(for further references see the PDB file header)

Molecule 1 - PRO-GRANZYME K
	Chains	:	A
	EC Number	:	3.4.21.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24C+
	Expression System Strain	:	B834 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GRANZYME K, GRANZYME 3, NK-TRYPTASE-2
	Tissue	:	BONE MARROW

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1MZA)

(no "Site" information available for 1MZA)

Asymmetric/Biological Unit

No.	Residues
1	A:42	-	A:58
2	A:136	-	A:201
3	A:168	-	A:182
4	A:191	-	A:220

Asymmetric/Biological Unit

No.	Residues
1	Asp A:173B	-	Pro A:174
2	Val A:243	-	Pro A:244
3	Pro A:244	-	Pro A:245

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	GRAK_HUMAN	27-259	1	A:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	GRAK_HUMAN	63-68	1	A:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	GRAK_HUMAN	208-219	1	A:189-200

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000231009	1	ENSE00000815160	chr5:54320081-54320214	134	GRAK_HUMAN	1-22	22	0	-	-
1.2	ENST00000231009	2	ENSE00000743501	chr5:54320488-54320635	148	GRAK_HUMAN	22-71	50	1	A:14-60A (gaps)	48
1.3b	ENST00000231009	3b	ENSE00000743506	chr5:54326262-54326412	151	GRAK_HUMAN	71-121	51	1	A:60A-107	51
1.4b	ENST00000231009	4b	ENSE00000743511	chr5:54327192-54327461	270	GRAK_HUMAN	122-211	90	1	A:108-192 (gaps)	92
1.5	ENST00000231009	5	ENSE00000815161	chr5:54329593-54330398	806	GRAK_HUMAN	212-264	53	1	A:193-248 (gaps)	58

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
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Chain A from PDB  Type:PROTEIN  Length:240
 aligned with GRAK_HUMAN | P49863 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:240
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264
          GRAK_HUMAN     25 MEIIGGKEVSPHSRPFMASIQYGGHHVCGGVLIDPQWVLTAAHCQYRFTKGQSPTVVLGAHSLSKNEASKQTLEIKKFIPFSRVTSDPQSNDIMLVKLQTAAKLNKHVKMLHIRSKTSLRSGTKCKVTGWGATDPDSLRPSDTLREVTVTVLSRKLCNSQSYYNGDPFITKDMVCAGDAKGQKDSCKGDSGGPLICKGVFHAIVSGGHECGVATKPGIYTLLTKKYQTWIKSNLVPPHTN  264
               SCOP domains d1mzaa_ A: Granzyme K                                                                                                                                                                                                                            SCOP domains
               CATH domains --1mzaA01     1mzaA02 A:28-120,A:233-245 Trypsin-like serine proteases                                        1mzaA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                          -1mzaA02      --- CATH domains
               Pfam domains --Trypsin-1mzaA01 A:16-238                                                                                                                                                                                                            ---------- Pfam domains
         Sec.struct. author ......ee........eeeeee..eeeeeeeeee..eeeehhhhh........eeeee............eeeeeeeeee.............eeeee.........................eeeeee...............eeeeeee.hhhhhh..............eeeee...............eeee..eeeeee............eeeee.hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --TRYPSIN_DOM  PDB: A:16-243 UniProt: 27-259                                                                                                                                                                                               ----- PROSITE (1)
                PROSITE (2) --------------------------------------TRYPSI-------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:14-60A (gaps) UniProt: 22-71  --------------------------------------------------Exon 1.4b  PDB: A:108-192 (gaps) UniProt: 122-211                                         Exon 1.5  PDB: A:193-248 (gaps) UniProt: 212-264      Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.3b  PDB: A:60A-107 UniProt: 71-121          ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1mza A   14 MEIIGGKEVSPHSRPFMASIQYGGHHVCGGVLIDPQWVLTAAHCQYRFTKGQSPTVVLGAHSLSKNEASKQTLEIKKFIPFSRVTSDPQSNDIMLVKLQTAAKLNKHVKMLHIRSKTSLRSGTKCKVTGWGATDPDSLRPSDTLREVTVTVLSRKLCNSQSYYNGDPFITKDMVCAGDAKGQKDSCKGDAGGPLICKGVFHAIVSGGHECGVATKPGIYTLLTKKYQTWIKSNLVPPHTN  248
                                    23        33 ||     44        54      |60D        70        80        90       100       110       120     ||131       141       151       161      170A|   || 177       187 ||    195      |209       220   |   229   |   238       248
                                                35|                     60A|||                                                               126|                 148A||                170A|   ||            188A|           202|       217| 223A      232A                
                                                 37                      60B||                                                                128                   149|                 170B   ||             188B            207        219                               
                                                                          60C|                                                                                       151                     173A|                                                                          
                                                                           60D                                                                                                                173B

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: All beta proteins (24004)

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Eukaryotic proteases (1343)

Protein domain: Granzyme K (2)

Human (Homo sapiens) [TaxId: 9606] (2)

d1mzaa_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Human (Homo sapiens) (615)

1a	1mzaA02	A:28-120,A:233-245
1b	1mzaA01	A:16-27,A:121-232

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Homo sapiens (Human) (339)

Trypsin-1mzaA01

A:16-238

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (GRAK_HUMAN | P49863)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1mza)

	Sites
(no "Sites" information available for 1mza)

	Cis Peptide Bonds
		Asp A:173B - Pro A:174	[ RasMol ]
		Pro A:244 - Pro A:245	[ RasMol ]
		Val A:243 - Pro A:244	[ RasMol ]

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	1mza
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	GRAK_HUMAN \| P49863
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	3.4.21.-
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	GRAK_HUMAN \| P49863
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UniProtKB/Swiss-Prot
	GRAK_HUMAN \| P49863	:	1mzd

1mzd	1MZD CONTAINS GRANZYME K AT 2.9A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (4, 4)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (4, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 2)

Pfam Domains (1, 1)

Gene Ontology (6, 6)

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