4AA8 - JenaLib

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Title :   BOVINE CHYMOSIN AT 1.8A RESOLUTION

Authors :   J. Langholm Jensen, A. Molgaard, J. C. Navarro Poulsen, J. M. Van Den M. Harboe, J. B. Simonsen, K. B. Qvist, S. Larsen

Date :   30 Nov 11 (Deposition) - 12 Dec 12 (Release) - 15 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Hydrolase, Aspartic Peptidase, Rennet (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Langholm Jensen, A. Molgaard, J. C. Navarro Poulsen, M. K. Harboe J. B. Simonsen, A. M. Lorentzen, K. Hjerno, J. M. Van Den Brink, K. B. Qvist, S. Larsen
Camel And Bovine Chymosin: The Relationship Between Their Structures And Cheese-Making Properties.
Acta Crystallogr. , Sect. D V. 69 901 2013
PubMed-ID: 23633601 | Reference-DOI: 10.1107/S0907444913003260

Molecule 1 - CHYMOSIN
	Chains	:	A
	EC Number	:	3.4.23.4
	Engineered	:	YES
	Expression System	:	ASPERGILLUS NIGER
	Expression System Taxid	:	5061
	Organ	:	ABOMASUM
	Organism Common	:	BOVINE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	PREPRORENNIN
	Tissue	:	MUCOSA

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	CL	8	Ligand/Ion	CHLORIDE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:14 , GLN A:15 , GLU A:118	BINDING SITE FOR RESIDUE CL A1324
2	AC2	SOFTWARE	GLN A:150 , ALA A:170 , ILE A:171 , HOH A:2186 , HOH A:2243	BINDING SITE FOR RESIDUE CL A1325
3	AC3	SOFTWARE	PRO A:128 , SER A:129 , HOH A:2203 , HOH A:2268	BINDING SITE FOR RESIDUE CL A1326
4	AC4	SOFTWARE	ASP A:151 , ALA A:313 , HOH A:2114 , HOH A:2230	BINDING SITE FOR RESIDUE CL A1327
5	AC5	SOFTWARE	ASN A:264 , HOH A:2260	BINDING SITE FOR RESIDUE CL A1328
6	AC6	SOFTWARE	LYS A:53 , ARG A:57 , CYS A:211 , GLN A:212	BINDING SITE FOR RESIDUE CL A1329
7	AC7	SOFTWARE	SER A:227 , GLN A:294 , HOH A:2303	BINDING SITE FOR RESIDUE CL A1330
8	AC8	SOFTWARE	SER A:273	BINDING SITE FOR RESIDUE CL A1331

Asymmetric Unit

No.	Residues
1	A:47	-	A:52
2	A:207	-	A:211
3	A:250	-	A:283

Asymmetric Unit

No.	Residues
1	Thr A:24	-	Pro A:25

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CHYM_BOVIN_001 *	G	302	D	CHYM_BOVIN	---	---	A	G	244	D
	* ID not provided by source

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

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CHYM_BOVIN_001 *	G	302	D	CHYM_BOVIN	---	---	A	G	244	D
	* ID not provided by source

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

Asymmetric Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	CHYM_BOVIN	74-378	1	A:16-320
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	CHYM_BOVIN	89-100 271-282	2	A:31-42 A:213-224

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	CHYM_BOVIN	74-378	2	A:16-320
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	CHYM_BOVIN	89-100 271-282	4	A:31-42 A:213-224

Asymmetric Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000013970	1	ENSBTAE00000266971	chr3:35631399-35631313	87	CHYM_BOVIN	1-21	21	0	-	-
1.2	ENSBTAT00000013970	2	ENSBTAE00000266969	chr3:35628381-35628231	151	CHYM_BOVIN	21-71	51	1	A:1-13	13
1.3	ENSBTAT00000013970	3	ENSBTAE00000114008	chr3:35627470-35627353	118	CHYM_BOVIN	72-111	40	1	A:14-53	40
1.4	ENSBTAT00000013970	4	ENSBTAE00000114011	chr3:35626285-35626167	119	CHYM_BOVIN	111-150	40	1	A:53-92	40
1.5	ENSBTAT00000013970	5	ENSBTAE00000266967	chr3:35624649-35624450	200	CHYM_BOVIN	151-217	67	1	A:93-159	67
1.6	ENSBTAT00000013970	6	ENSBTAE00000114017	chr3:35623869-35623756	114	CHYM_BOVIN	217-255	39	1	A:159-197	39
1.7	ENSBTAT00000013970	7	ENSBTAE00000114020	chr3:35622433-35622289	145	CHYM_BOVIN	255-303	49	1	A:197-245	49
1.8	ENSBTAT00000013970	8	ENSBTAE00000114021	chr3:35621673-35621575	99	CHYM_BOVIN	304-336	33	1	A:246-278	33
1.9	ENSBTAT00000013970	9	ENSBTAE00000266965	chr3:35620863-35620595	269	CHYM_BOVIN	337-381	45	1	A:279-323	45

Asymmetric 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:323
 aligned with CHYM_BOVIN | P00794 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:323
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378   
           CHYM_BOVIN    59 GEVASVPLTNYLDSQYFGKIYLGTPPQEFTVLFDTGSSDFWVPSIYCKSNACKNHQRFDPRKSSTFQNLGKPLSIHYGTGSMQGILGYDTVTVSNIVDIQQTVGLSTQEPGDVFTYAEFDGILGMAYPSLASEYSIPVFDNMMNRHLVAQDLFSVYMDRNGQESMLTLGAIDPSYYTGSLHWVPVTVQQYWQFTVDSVTISGVVVACEGGCQAILDTGTSKLVGPSSDILNIQQAIGATQNQYGEFDIDCDNLSYMPTVVFEINGKMYPLTPSAYTSQDQGFCTSGFQSENHSQKWILGDVFIREYYSVFDRANNLVGLAKAI 381
               SCOP domains d4aa8a_ A: Chymosin (synonym: renin)                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........eeeee....eeeeeeee.....eee......hhhhhh....hhhhh................eeeeeeeeeeeeee..eeeeeeeeeeeee............eeee..hhhhh.....hhhhhhhhh......eeeee........eeee...hhh.eeeeeeeee.......eeee.eeee..eeee....eeeee......eeeehhhhhhhhhhh..ee.....eeehhhhhhhh..eeeee..eeeeehhhhheee....eee.eeee.....eeehhhhhh.eeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------PEPTIDASE_A1  PDB: A:16-320 UniProt: 74-378                                                                                                                                                                                                                                                                      --- PROSITE (1)
                PROSITE (2) ------------------------------ASP_PROTEASE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE--------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2     Exon 1.3  PDB: A:14-53 UniProt: 72-111  ---------------------------------------Exon 1.5  PDB: A:93-159 UniProt: 151-217                           -------------------------------------Exon 1.7  PDB: A:197-245 UniProt: 255-303        Exon 1.8  PDB: A:246-278         Exon 1.9  PDB: A:279-323 UniProt: 337-381     Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------Exon 1.4  PDB: A:53-92 UniProt: 111-150 ------------------------------------------------------------------Exon 1.6  PDB: A:159-197               ------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 4aa8 A   1 GEVASVPLTNYLDSQYFGKIYLGTPPQEFTVLFDTGSSDFWVPSIYCKSNACKNHQRFDPRKSSTFQNLGKPLSIHYGTGSMQGILGYDTVTVSNIVDIQQTVGLSTQEPGDVFTYAEFDGILGMAYPSLASEYSIPVFDNMMNRHLVAQDLFSVYMDRNGQESMLTLGAIDPSYYTGSLHWVPVTVQQYWQFTVDSVTISGVVVACEGGCQAILDTGTSKLVGPSSDILNIQQAIGATQNQYGEFDIDCDNLSYMPTVVFEINGKMYPLTPSAYTSQDQGFCTSGFQSENHSQKWILGDVFIREYYSVFDRANNLVGLAKAI 323
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Acid proteases (1120)

Superfamily: Acid proteases (1120)

Family: Pepsin-like (505)

Protein domain: Chymosin (synonym: renin) (67)

Cow (Bos taurus) [TaxId: 9913] (6)

d4aa8a_

(no "CATH Domain" information available for 4AA8)

(no "Pfam Domain" information available for 4AA8)

Asymmetric Unit(hide GO term definitions)

Chain A (CHYM_BOVIN | P00794)

molecular function
	GO:0004190	aspartic-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
	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.
biological process
	GO:0007586	digestion	The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
	GO:0030163	protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Asymmetric Unit
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		Thr A:24 - Pro A:25	[ RasMol ]

Biological Unit
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	4aa8
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UniProtKB/Swiss-Prot
	CHYM_BOVIN \| P00794	:	1cms 1czi 3cms 4auc 4cms

1cms	CHYMOSIN B (FORMERLY KNOWN AS RENNIN)
1czi	CHYMOSIN COMPLEX WITH THE INHIBITOR CP-113972
3cms	CHYMOSIN B (FORMERLY KNOWN AS RENNIN) MUTANT WITH VAL 111 REPLACED BY PHE (V111F)
4aa9	CAMEL CHYMOSIN AT 1.6A RESOLUTION
4cms	CHYMOSIN B (FORMERLY KNOWN AS RENNIN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (3, 3)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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Exons (8, 8)

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Gene Ontology (6, 6)

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