1UH9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RHIZOPUSPEPSIN AT PH 7.0

Authors :   B. V. L. S. Prasad, K. Suguna

Date :   26 Jun 03 (Deposition) - 26 Jun 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

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

Reference :   B. V. Prasad, K. Suguna
Effect Of Ph On The Structure Of Rhizopuspepsin.
Acta Crystallogr. , Sect. D V. 59 1755 2003
PubMed-ID: 14501114 | Reference-DOI: 10.1107/S0907444903016068
(for further references see the PDB file header)

Molecule 1 - HIZOPUSPEPSIN I
	Chains	:	A
	EC Number	:	3.4.23.6
	Organism Scientific	:	RHIZOPUS MICROSPORUS VAR. CHINENSIS
	Organism Taxid	:	4843
	Strain	:	VAR. CHINENSIS
	Synonym	:	RHIZOPUSPEPSIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1UH9)

(no "Site" information available for 1UH9)

Asymmetric/Biological Unit

No.	Residues
1	A:48	-	A:51
2	A:252	-	A:285

Asymmetric/Biological Unit

No.	Residues
1	Thr A:25	-	Pro A:26
2	Val A:315	-	Pro A:316

Asymmetric/Biological Unit (8, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CARP_RHICH_001 *	V	83	I	CARP_RHICH	---	---	A	I	15	I
2	UniProt	VAR_CARP_RHICH_002 *	K	129	N	CARP_RHICH	---	---	A	N	61	N
3	UniProt	VAR_CARP_RHICH_003 *	N	184	S	CARP_RHICH	---	---	A	S	116	S
4	UniProt	VAR_CARP_RHICH_004 *	S	230	K	CARP_RHICH	---	---	A	K	162	K
5	UniProt	VAR_CARP_RHICH_005 *	V	298	I	CARP_RHICH	---	---	A	I	230	I
6	UniProt	VAR_CARP_RHICH_006 *	S	309	Y	CARP_RHICH	---	---	A	S	241	Y
7	UniProt	VAR_CARP_RHICH_007 *	N	361	D	CARP_RHICH	---	---	A	N	293	D
8	UniProt	VAR_CARP_RHICH_008 *	Q	393	E	CARP_RHICH	---	---	A	E	325	E
	* ID not provided by source

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

Asymmetric/Biological Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	CARP_RHICH	85-389	1	A:17-321
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	CARP_RHICH	100-111 283-294	2	A:32-43 A:215-226

(no "Exon" information available for 1UH9)

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:325
 aligned with CARP_RHICH | P06026 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:325
                                    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       388     
           CARP_RHICH    69 AGVGTVPMTDYGNDVEYYGQVTIGTPGKKFNLDFDTGSSDLWIASTLCTNCGSRQTKYDPKQSSTYQADGRTWSISYGDGSSASGILAKDNVNLGGLLIKGQTIELAKREAASFANGPNDGLLGLGFDTITTVRGVKTPMDNLISQGLISRPIFGVYLGKASNGGGGEYIFGGYDSTKFKGSLTTVPIDNSRGWWGITVDRATVGTSTVASSFDGILDTGTTLLILPNNVAASVARAYGASDNGDGTYTISCDTSRFKPLVFSINGASFQVSPDSLVFEEYQGQCIAGFGYGNFDFAIIGDTFLKNNYVVFNQGVPEVQIAPVAQ 393
               SCOP domains d1uh9a_ A: Acid protease                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -----1uh9A01 A:6-174 Acid Proteases                                                                                                                                           1uh9A02 A:175-323 Acid Proteases                                                                                                                     -- CATH domains
               Pfam domains ---------------Asp-1uh9A01 A:16-323                                                                                                                                                                                                                                                                                                -- Pfam domains
         Sec.struct. author ....eeeeeee....eeeeeeee....eeeeeeee......eee..............hhhhh...eeeeeeeeee.....eeeeeeeeeeeee..eeeeeeeeeeeeeehhhhhh....eeee..hhhhh......hhhhhhhhh......eeeeee.hhhhh..eeeee...hhhhh....eeee........eeee.eeee..eeee..eeeee......eeeehhhhhhhhhhh..ee.....eee..hhhhh..eeeee..eeeeehhhh.eeeee..eeee.eeee....eeehhhhhh.eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------I---------------------------------------------N------------------------------------------------------S---------------------------------------------K-------------------------------------------------------------------I----------Y---------------------------------------------------D-------------------------------E SAPs(SNPs)
                PROSITE (1) ----------------PEPTIDASE_A1  PDB: A:17-321 UniProt: 85-389                                                                                                                                                                                                                                                                      ---- PROSITE (1)
                PROSITE (2) -------------------------------ASP_PROTEASE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE--------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uh9 A   1 AGVGTVPMTDYGNDIEYYGQVTIGTPGKKFNLDFDTGSSDLWIASTLCTNCGSRQTKYDPNQSSTYQADGRTWSISYGDGSSASGILAKDNVNLGGLLIKGQTIELAKREAASFASGPNDGLLGLGFDTITTVRGVKTPMDNLISQGLISRPIFGVYLGKAKNGGGGEYIFGGYDSTKFKGSLTTVPIDNSRGWWGITVDRATVGTSTVASSFDGILDTGTTLLILPNNIAASVARAYGASDNGDGTYTISCDTSRFKPLVFSINGASFQVSPDSLVFEEFQGQCIAGFGYGNWDFAIIGDTFLKNNYVVFNQGVPEVQIAPVAE 325
                                    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

Chain A from PDB  Type:PROTEIN  Length:325
 aligned with Q02016_RHICH | Q02016 from UniProtKB/TrEMBL  Length:340

    Alignment length:325
                                                                                                                                                                                                                                                                                                          340                                                    
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337  |      -         -         -         -         -     
         Q02016_RHICH    68 AGVGTVPMTDYGNDIEYYGQVTIGTPGKKFNLDFDTGSSDLWIASTLCTNCGSRQTKYDPNQSSTYQADGRTWSISYGDGSSASGILAKDNVNLGGLLIKGQTIELAKREAASFASGPNDGLLGLGFDTITTVRGVKTPMDNLISQGLISRPIFGVYLGKAKNGGGGEYIFGGYDSTKFKGSLTTVPIDNSRGWWGITVDRATVGTSTVASSFDGILDTGTTLLILPNNIAASVARAYGAYDNGDGTYTISCDTSRFKPLVFSINGASFQVSP----------------------------------------------------   -
               SCOP domains d1uh9a_ A: Acid protease                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -----1uh9A01 A:6-174 Acid Proteases                                                                                                                                           1uh9A02 A:175-323 Acid Proteases                                                                                                                     -- CATH domains
               Pfam domains ---------------Asp-1uh9A01 A:16-323                                                                                                                                                                                                                                                                                                -- Pfam domains
         Sec.struct. author ....eeeeeee....eeeeeeee....eeeeeeee......eee..............hhhhh...eeeeeeeeee.....eeeeeeeeeeeee..eeeeeeeeeeeeeehhhhhh....eeee..hhhhh......hhhhhhhhh......eeeeee.hhhhh..eeeee...hhhhh....eeee........eeee.eeee..eeee..eeeee......eeeehhhhhhhhhhh..ee.....eee..hhhhh..eeeee..eeeeehhhh.eeeee..eeee.eeee....eeehhhhhh.eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------I---------------------------------------------N------------------------------------------------------S---------------------------------------------K-------------------------------------------------------------------I----------Y---------------------------------------------------D-------------------------------E SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uh9 A   1 AGVGTVPMTDYGNDIEYYGQVTIGTPGKKFNLDFDTGSSDLWIASTLCTNCGSRQTKYDPNQSSTYQADGRTWSISYGDGSSASGILAKDNVNLGGLLIKGQTIELAKREAASFASGPNDGLLGLGFDTITTVRGVKTPMDNLISQGLISRPIFGVYLGKAKNGGGGEYIFGGYDSTKFKGSLTTVPIDNSRGWWGITVDRATVGTSTVASSFDGILDTGTTLLILPNNIAASVARAYGASDNGDGTYTISCDTSRFKPLVFSINGASFQVSPDSLVFEEFQGQCIAGFGYGNWDFAIIGDTFLKNNYVVFNQGVPEVQIAPVAE 325
                                    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/Biological 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: Acid protease (44)

Bread mold (Rhizopus chinensis) [TaxId: 4843] (8)

d1uh9a_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Cathepsin D, subunit A; domain 1 (745)

Homologous Superfamily: Acid Proteases (745)

Chinensis (Rhizopus microsporus var) (5)

1a	1uh9A01	A:6-174
1b	1uh9A02	A:175-323

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_AA (368)

Family: Asp (155)

Rhizopus chinensis (Bread mold) (3)

Asp-1uh9A01

A:16-323

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q02016_RHICH | Q02016)

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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Chain A (CARP_RHICH | P06026)

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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1uh9)

	Sites
(no "Sites" information available for 1uh9)

	Cis Peptide Bonds
		Thr A:25 - Pro A:26	[ RasMol ]
		Val A:315 - Pro A:316	[ RasMol ]

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	1uh9
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	CARP_RHICH \| P06026
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	Q02016_RHICH \| Q02016
		Comparative Protein Structure Models	:	ModBase
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	3.4.23.6
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		Pathway	:	KEGG \| MetaCyc

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		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	CARP_RHICH \| P06026	:	1uh7 1uh8 2apr 3apr 4apr 5apr 6apr
	Q02016_RHICH \| Q02016	:	1uh7 1uh8

1uh7	CRYSTAL STRUCTURE OF RHIZOPUSPEPSIN AT PH 4.6
1uh8	CRYSTAL STRUCTURE OF RHIZOPUSPEPSIN AT PH 8.0
2apr	CRYSTAL STRUCTURE OF RHIZOPUSPEPSIN AT PH 6.0

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 8)

PROSITE Motifs (2, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 2)

Pfam Domains (1, 1)

Gene Ontology (4, 8)

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Related Entries Specified in the PDB File