2NQG - JenaLib

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Title :   CALPAIN 1 PROTEOLYTIC CORE INACTIVATED BY WR18(S,S), AN EPOXYSUCCINYL-TYPE INHIBITOR.

Authors :   D. Cuerrier, P. L. Davies, R. L. Campbell, T. Moldoveanu

Date :   31 Oct 06 (Deposition) - 09 Jan 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.04

Chains :   Asym./Biol. Unit : A

Keywords :   Epoxide, Epoxysuccinyl, Protease, Peptidase, Proteinase, Inactivator, Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Cuerrier, T. Moldoveanu, R. L. Campbell, J. Kelly, B. Yoruk, S. H. L. Verhelst, D. Greenbaum, M. Bogyo, P. L. Davies
Development Of Calpain-Specific Inactivators By Screening Of Positional Scanning Epoxide Libraries
J. Biol. Chem. V. 282 9600 2007
PubMed-ID: 17218315 | Reference-DOI: 10.1074/JBC.M610372200
(for further references see the PDB file header)

Molecule 1 - CALPAIN-1 CATALYTIC SUBUNIT
	Chains	:	A
	EC Number	:	3.4.22.52
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET24D
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	CALPAIN CATALYTIC DOMAIN, RESIDUES 27-356
	Gene	:	CAPN1, CLS1
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	CALPAIN-1 LARGE SUBUNIT, CALCIUM-ACTIVATED NEUTRAL PROTEINASE 1, CANP 1, CALPAIN MU-TYPE, MUCANP, MICROMOLAR-CALPAIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	NQG	1	Ligand/Ion	5-AZANYLIDYNE-N-[(2S)-4-ETHOXY-2-HYDROXY-4-OXOBUTANOYL]-L-NORVALYL-L-ARGINYL-L-TRYPTOPHANAMIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:99 , GLY A:101 , ASP A:106 , GLU A:185 , HOH A:518 , HOH A:612	BINDING SITE FOR RESIDUE CA A 401
2	AC2	SOFTWARE	GLU A:302 , ASP A:309 , MET A:329 , ASP A:331 , GLU A:333 , HOH A:627	BINDING SITE FOR RESIDUE CA A 402
3	AC3	SOFTWARE	GLN A:109 , GLY A:113 , ASP A:114 , CYS A:115 , TRP A:116 , GLY A:207 , GLY A:208 , CYS A:209 , THR A:210 , SER A:251 , ILE A:252 , ASN A:253 , GLY A:271 , HIS A:272 , GLN A:287 , TRP A:298 , ARG A:339 , LYS A:347 , HOH A:544 , HOH A:571	BINDING SITE FOR RESIDUE NQG A 501

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

(no "Cis Peptide Bond" information available for 2NQG)

(no "SAP(SNP)/Variant" information available for 2NQG)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CALPAIN_CAT	PS50203	Cysteine proteinase, calpain-type, catalytic domain profile.	CAN1_RAT	55-354	1	A:55-354
2	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	CAN1_RAT	109-120	1	A:109-120

(no "Exon" information available for 2NQG)

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:322
 aligned with CAN1_RAT | P97571 from UniProtKB/Swiss-Prot  Length:713

    Alignment length:322
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352  
             CAN1_RAT    33 NAIKYLGQDYENLRARCLQNGVLFQDDAFPPVSHSLGFKELGPNSSKTYGIKWKRPTELLSNPQFIVDGATRTDICQGALGDCWLLAAIASLTLNETILHRVVPYGQSFQEGYAGIFHFQLWQFGEWVDVVVDDLLPTKDGKLVFVHSAQGNEFWSALLEKAYAKVNGSYEALSGGCTSEAFEDFTGGVTEWYDLQKAPSDLYQIILKALERGSLLGCSINISDIRDLEAITFKNLVRGHAYSVTDAKQVTYQGQRVNLIRMRNPWGEVEWKGPWSDNSYEWNKVDPYEREQLRVKMEDGEFWMSFRDFIREFTKLEICNLT 354
               SCOP domains d2nqga_ A: Calpain large subunit, catalytic domain (domain II)                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------Peptidase_C2-2nqgA01 A:55-354                                                                                                                                                                                                                                                                                Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhhhhh...........hhhhhh.......hhhhhh.eeehhhhhh..........hhhhh......hhhhhhhhhhhh.hhhhhhhhh............eeeeeeee..eeeeeeee..eeee..ee..........hhhhhhhhhhhhhhh.hhhhh..hhhhhhhhh...eeeeee.hhh..hhhhhhhhhhhh..eeeee......................eeeeeeeeeee..eeeeeeeee................hhhhhhhhhhhhhhh......eeeeehhhhhhhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------CALPAIN_CAT  PDB: A:55-354 UniProt: 55-354                                                                                                                                                                                                                                                                   PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nqg A  33 NAIKYLGQDYENLRARCLQNGVLFQDDAFPPVSHSLGFKELGPNSSKTYGIKWKRPTELLSNPQFIVDGATRTDICQGALGDCWLLAAIASLTLNETILHRVVPYGQSFQEGYAGIFHFQLWQFGEWVDVVVDDLLPTKDGKLVFVHSAQGNEFWSALLEKAYAKVNGSYEALSGGCTSEAFEDFTGGVTEWYDLQKAPSDLYQIILKALERGSLLGCSINISDIRDLEAITFKNLVRGHAYSVTDAKQVTYQGQRVNLIRMRNPWGEVEWKGPWSDNSYEWNKVDPYEREQLRVKMEDGEFWMSFRDFIREFTKLEICNLT 354
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352

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) (23004)

Fold: Cysteine proteinases (392)

Superfamily: Cysteine proteinases (392)

Family: Calpain large subunit, catalytic domain (domain II) (19)

Protein domain: Calpain large subunit, catalytic domain (domain II) (19)

Norway rat (Rattus norvegicus), mu-type [TaxId: 10116] (10)

d2nqga_

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_CA (169)

Family: Peptidase_C2 (15)

Rattus norvegicus (Rat) (10)

Peptidase_C2-2nqgA01

A:55-354

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CAN1_RAT | P97571)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0004198	calcium-dependent cysteine-type endopeptidase activity	Catalysis of the hydrolysis of nonterminal peptide bonds in a polypeptide chain by a mechanism using a cysteine residue at the enzyme active center, and requiring the presence of calcium.
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0008092	cytoskeletal protein binding	Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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).
biological process
	GO:0016540	protein autoprocessing	Processing which a protein carries out itself. This involves actions such as the autolytic removal of residues to generate the mature form of the protein.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2nqg)

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	2nqg
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	CAN1_RAT \| P97571
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	3.4.22.52
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UniProtKB/Swiss-Prot
	CAN1_RAT \| P97571	:	1kxr 1qxp 1tl9 1tlo 2g8e 2g8j 2nqi 2r9c 2r9f

1kxr	CRYSTAL STRUCTURE OF THE SAME PROTEIN FRAGMENT, UNCOMPLEXED.
1tl9	CRYSTAL STRUCTURE OF THE SAME PROTEIN FRAGMENT, COMPLEXED WITH LEUPEPTIN, AN ALDEHYDE INHIBITOR.
1tlo	CRYSTAL STRUCTURE OF THE SAME PROTEIN FRAGMENT, INACTIVATED BY E-64, ANOTHER EPOXYSUCCINYL INHIBITOR.
1zcm	CRYSTAL STRUCTURE OF THE HUMAN ISOFORM OF THE SAME PROTEIN FRAGMENT, INACTIVATED BY Z-LLY-FMK, A FLUOROMETHYL KETONE INHIBITOR.
2g8e	CRYSTAL STRUCTURE OF THE SAME PROTEIN FRAGMENT, COMPLEXED WITH SNJ-1715, A CYCLIC HEMIACETAL INHIBITOR.
2g8j	CRYSTAL STRUCTURE OF THE SAME PROTEIN FRAGMENT, COMPLEXED WITH SNJ-1945, AN ALPHA-KETOAMIDE INHIBITOR.
2nqi	CRYSTAL STRUCTURE OF THE SAME PROTEIN FRAGMENT, INACTIVATED BY WR13(R,R), ANOTHER EPOXYSUCCINYL INHIBITOR WITH OPPOSITE STEREOCHEMISTRY.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (14, 14)

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