3PRO - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   ALPHA-LYTIC PROTEASE COMPLEXED WITH C-TERMINAL TRUNCATED PRO REGION

Authors :   N. K. Sauter, T. Mau, S. D. Rader, D. A. Agard

Date :   26 Aug 98 (Deposition) - 27 Apr 99 (Release) - 06 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)

Keywords :   Pro Region, Foldase, Protein Folding, Serine Protease, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. K. Sauter, T. Mau, S. D. Rader, D. A. Agard
Structure Of Alpha-Lytic Protease Complexed With Its Pro Region.
Nat. Struct. Biol. V. 5 945 1998
PubMed-ID: 9808037 | Reference-DOI: 10.1038/2919

Molecule 1 - ALPHA-LYTIC PROTEASE
	Cell Line	:	B834
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CULTURE FILTRATE
	Expression System Plasmid	:	PT7PRO-3
	Expression System Strain	:	B834 (DE3) PLYSS
	Expression System Taxid	:	562
	Fragment	:	MATURE PROTEASE
	Mutation	:	YES
	Organism Scientific	:	LYSOBACTER ENZYMOGENES
	Organism Taxid	:	69

Molecule 2 - ALPHA-LYTIC PROTEASE
	Cell Line	:	B834
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	INCLUSION BODIES
	Expression System Plasmid	:	PT7PRO-3
	Expression System Strain	:	B834 (DE3) PLYSS
	Expression System Taxid	:	562
	Fragment	:	PRO REGION
	Organism Scientific	:	LYSOBACTER ENZYMOGENES
	Organism Taxid	:	69
	Other Details	:	T7 EXPRESSION SYSTEM

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	AES	2	Ligand/Ion	4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	AES	1	Ligand/Ion	4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	AES	1	Ligand/Ion	4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:36 , MET A:138 , GLY A:139 , ARG A:140 , ASP A:142 , SER A:143 , ALA A:158 , SER A:159 , GLY A:160 , GLY A:161 , VAL A:163 , LYS C:162 , LEU C:163	BINDING SITE FOR RESIDUE AES A 199
2	AC2	SOFTWARE	HIS B:36 , MET B:138 , GLY B:139 , ARG B:140 , ASP B:142 , SER B:143 , SER B:159 , GLY B:160 , GLY B:161 , VAL B:163 , HOH B:223 , LYS D:162 , LEU D:163	BINDING SITE FOR RESIDUE AES B 199

Asymmetric Unit

No.	Residues
1	A:17	-	A:37
2	A:101	-	A:111
3	A:137	-	A:170
4	B:17	-	B:37
5	B:101	-	B:111
6	B:137	-	B:170

Asymmetric Unit

No.	Residues
1	Phe A:59	-	Pro A:60
2	Phe B:59	-	Pro B:60

(no "SAP(SNP)/Variant" information available for 3PRO)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	PRLA_LYSEN	231-236	2	A:32-37 B:32-37
2	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	PRLA_LYSEN	336-347	2	A:137-148 B:137-148

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	PRLA_LYSEN	231-236	1	A:32-37 -
2	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	PRLA_LYSEN	336-347	1	A:137-148 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	PRLA_LYSEN	231-236	1	- B:32-37
2	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	PRLA_LYSEN	336-347	1	- B:137-148

(no "Exon" information available for 3PRO)

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:198
 aligned with PRLA_LYSEN | P00778 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:198
                                   209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389        
           PRLA_LYSEN   200 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACMGRGDSGGSWITSAGQAQGVMSGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG 397
               SCOP domains d3proa_ A: alpha-Lytic protease                                                                                                                                                                        SCOP domains
               CATH domains --3proA01 A:3-76,A:184-196 Trypsin-like serine proteases                    3proA02 A:77-183 Trypsin-like serine proteases                                                             3proA01      -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeee...eeee..eeeee..eeeeee.hhh.....eeee..eeeeeeeeee.....eeeeee........eeee..eeee...........eeeeee...eeeeee.......eee..eee...eee...........eeee....eeeeeeee............hhh..eeeeehhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------TRYPSI---------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pro A   1 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACMGRGDSGGSWITSAGQAQGVASGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG 198
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:198
 aligned with PRLA_LYSEN | P00778 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:198
                                   209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389        
           PRLA_LYSEN   200 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACMGRGDSGGSWITSAGQAQGVMSGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG 397
               SCOP domains d3prob_ B: alpha-Lytic protease                                                                                                                                                                        SCOP domains
               CATH domains --3proB01 B:3-76,B:184-196 Trypsin-like serine proteases                    3proB02 B:77-183 Trypsin-like serine proteases                                                             3proB01      -- CATH domains
           Pfam domains (1) --Trypsin-3proB01 B:3-179                                                                                                                                                          ------------------- Pfam domains (1)
           Pfam domains (2) --Trypsin-3proB02 B:3-179                                                                                                                                                          ------------------- Pfam domains (2)
         Sec.struct. author .......eeee...eeee..eeeee..eeeeee.hhh.....eeee..eeeeeeeeee.....eeeeee........eeee..eeee...........eeeeee...eeeeee.......eee..eee...eee...........eee.....eeeeeeee............hhh..eeeeehhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------TRYPSI---------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pro B   1 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACMGRGDSGGSWITSAGQAQGVASGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG 198
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain C from PDB  Type:PROTEIN  Length:150
 aligned with PRLA_LYSEN | P00778 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:158
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188        
           PRLA_LYSEN    39 PQLKFAMQRDLGIFPTQLPQYLQTEKLARTQAAAIEREFGAQFAGSWIERNEDGSFKLVAATSGARKSSTLGGVEVRNVRYSLKQLQSAMEQLDAGANARVKGVSKPLDGVQSWYVDPRSNAVVVKVDDGATEAGVDFVALSGADSAQVRIESSPGKL 196
               SCOP domains d3proc1 C:6-85 Alpha-lytic protease prodomain                                   d3proc2 C:86-163 Al        pha-lytic protease prodomain                        SCOP domains
               CATH domains 3proC01 C:6-84  [code=3.30.300.50, no name defined]                            3proC02 C:85-162  [c        ode=3.30.300.50, no name defined]                 - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.....eeeeeee...........eeeee....hhhhhhhhhhhhhhhh.--------...eeeeeeehhh.eeeeeee...hhhhhhhhhhh......eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pro C   6 PQLKFAMQRDLGIFPTQLPQYLQTEKLARTQAAAIEREFGAQFAGSWIERNEDGSFKLVAATSGARKSSTLGGVEVRNVRYSLKQLQSAMEQLDAGANA--------LDGVQSWYVDPRSNAVVVKVDDGATDAGVDFVALSGADSAQVRIESSPGKL 163
                                    15        25        35        45        55        65        75        85        95        |-       115       125       135       145       155        
                                                                                                                            104      113

Chain D from PDB  Type:PROTEIN  Length:152
 aligned with PRLA_LYSEN | P00778 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:161
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195 
           PRLA_LYSEN    36 QVDPQLKFAMQRDLGIFPTQLPQYLQTEKLARTQAAAIEREFGAQFAGSWIERNEDGSFKLVAATSGARKSSTLGGVEVRNVRYSLKQLQSAMEQLDAGANARVKGVSKPLDGVQSWYVDPRSNAVVVKVDDGATEAGVDFVALSGADSAQVRIESSPGKL 196
               SCOP domains d3prod1 D:3-85 Alpha-lytic protease prodomain                                      d3prod2 D:86-163 A         lpha-lytic protease prodomain                       SCOP domains
               CATH domains ---3proD01 D:6-84  [code=3.30.300.50, no name defined]                            3proD02 D:85-162  [         code=3.30.300.50, no name defined]                - CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------Pro_Al_protease-3p         roD01 D:86-155                             -------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------Pro_Al_protease-3p         roD02 D:86-155                             -------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------Pro_Al_protease-3p         roD03 D:86-155                             -------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------Pro_Al_protease-3p         roD04 D:86-155                             -------- Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhh...eeeee.....eeeeeee...........eeeee....hhhhhhhhhhhhhhh.---------...eeeeeeehhh.eeeeeee...hhhhhhhhhhh...hhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pro D   3 QVDPQLKFAMQRDLGIFPTQLPQYLQTEKLARTQAAAIEREFGAQFAGSWIERNEDGSFKLVAATSGARKSSTLGGVEVRNVRYSLKQLQSAMEQLDAGAN---------LDGVQSWYVDPRSNAVVVKVDDGATDAGVDFVALSGADSAQVRIESSPGKL 163
                                    12        22        32        42        52        62        72        82        92       102|        -|      122       132       142       152       162 
                                                                                                                              103       113

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: GMP Synthetase; Chain A, domain 3 (192)

Homologous Superfamily: [code=3.30.300.50, no name defined] (3)

Lysobacter enzymogenes. Organism_taxid: 69. Cell_line: b834. (2)

1a	3proC02	C:85-162
1b	3proD02	D:85-162
1c	3proC01	C:6-84
1d	3proD01	D:6-84

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Lysobacter enzymogenes. Organism_taxid: 69. Cell_line: b834. (1)

2a	3proA02	A:77-183
2b	3proB02	B:77-183
2c	3proA01	A:3-76,A:184-196
2d	3proB01	B:3-76,B:184-196

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Lysobacter enzymogenes (16)

1a	Trypsin-3proB01	B:3-179
1b	Trypsin-3proB02	B:3-179

Clan: no clan defined [family: Pro_Al_protease] (2)

Family: Pro_Al_protease (2)

Lysobacter enzymogenes (2)

2a	Pro_Al_protease-3proD01	D:86-155
2b	Pro_Al_protease-3proD02	D:86-155
2c	Pro_Al_protease-3proD03	D:86-155
2d	Pro_Al_protease-3proD04	D:86-155

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PRLA_LYSEN | P00778)

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 Unit
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Description

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