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Title :   CRYSTAL STRUCTURE OF A NOVEL INTRACELLULAR PROTEASE FROM PYROCOCCUS HORIKOSHII AT 2 A RESOLUTION

Authors :   X. Du, I-G. Choi, R. Kim, J. Jancarik, S. -H. Kim, Berkeley Structural Center (Bsgc)

Date :   19 Oct 00 (Deposition) - 08 Nov 00 (Release) - 08 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Intracellular Protease, Atp-Independent Intracellular Protease, Protease, Catalytical Triad, Pfpi, Cysteine Protease, Nucleophile Elbow, Structural Genomics, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Du, I. G. Choi, R. Kim, W. Wang, J. Jancarik, H. Yokota, S. -H. Kim
Crystal Structure Of An Intracellular Protease From Pyrococcus Horikoshii At 2-A Resolution.
Proc. Natl. Acad. Sci. Usa V. 97 14079 2000
PubMed-ID: 11114201 | Reference-DOI: 10.1073/PNAS.260503597

Molecule 1 - PROTEASE I
	Chains	:	A, B, C
	EC Number	:	3.2.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	B834(DE3)/SJS1244
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PH1704
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	53953

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 13)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 26)

No.	Name	Count	Type	Full Name
1	MSE	24	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:313 , GLY B:331 , HOH B:744 , ARG C:513	BINDING SITE FOR RESIDUE SO4 B 600

(no "SS Bond" information available for 1G2I)

(no "Cis Peptide Bond" information available for 1G2I)

(no "SAP(SNP)/Variant" information available for 1G2I)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_C56_PFPI	PS51276	PfpI endopeptidase domain profile.	PFPI_PYRHO	1-166	3	A:1-166 B:201-366 C:401-566

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_C56_PFPI	PS51276	PfpI endopeptidase domain profile.	PFPI_PYRHO	1-166	6	A:1-166 B:201-366 C:401-566

(no "Exon" information available for 1G2I)

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:166
 aligned with PFPI_PYRHO | O59413 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      
           PFPI_PYRHO     1 MKVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFERGTITGKHGYSVKVDLTFDKVNPEEFDALVLPGGRAPERVRLNEKAVSIARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAGVEWVDAEVVVDGNWVSSRVPADLYAWMREFVKLLK 166
               SCOP domains d1g2ia_ A: Intracellular protease                                                                                                                                      SCOP domains
               CATH domains -1g2iA00 A:2-166  [code=3.40.50.880, no name defined]                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhh..eeeeee...eeee.....eeee.ee.hhhhhhhh.eeee...hhhhhhh.hhhhhhhhhhhhhh...eeee...hhhhhhhh.....ee..hhhhhhhhhhh..ee.....eee..eeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PEPTIDASE_C56_PFPI  PDB: A:1-166 UniProt: 1-166                                                                                                                        PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g2i A   1 mKVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFERGTITGKHGYSVKVDLTFDKVNPEEFDALVLPGGRAPERVRLNEKAVSIARKmFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDmINAGVEWVDAEVVVDGNWVSSRVPADLYAWmREFVKLLK 166
                            |       10        20        30        40        50        60        70        80        90       100       110       120      |130       140       150       160      
                            |                                                                                      89-MSE                               127-MSE                        158-MSE    
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:166
 aligned with PFPI_PYRHO | O59413 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      
           PFPI_PYRHO     1 MKVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFERGTITGKHGYSVKVDLTFDKVNPEEFDALVLPGGRAPERVRLNEKAVSIARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAGVEWVDAEVVVDGNWVSSRVPADLYAWMREFVKLLK 166
               SCOP domains d1g2ib_ B: Intracellular protease                                                                                                                                      SCOP domains
               CATH domains -1g2iB00 B:202-366  [code=3.40.50.880, no name defined]                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhh..eeeeee...eeee.....eeee.ee.hhhhhhhh.eeee....hhhhhh.hhhhhhhhhhhhhh...eeee...hhhhhhhh.....ee..hhhhhhhhhhh..ee.....eee..eeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PEPTIDASE_C56_PFPI  PDB: B:201-366 UniProt: 1-166                                                                                                                      PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g2i B 201 mKVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFERGTITGKHGYSVKVDLTFDKVNPEEFDALVLPGGRAPERVRLNEKAVSIARKmFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDmINAGVEWVDAEVVVDGNWVSSRVPADLYAWmREFVKLLK 366
                            |      210       220       230       240       250       260       270       280       290       300       310       320      |330       340       350       360      
                          201-MSE                                                                                 289-MSE                               327-MSE                        358-MSE

Chain C from PDB  Type:PROTEIN  Length:166
 aligned with PFPI_PYRHO | O59413 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      
           PFPI_PYRHO     1 MKVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFERGTITGKHGYSVKVDLTFDKVNPEEFDALVLPGGRAPERVRLNEKAVSIARKMFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDMINAGVEWVDAEVVVDGNWVSSRVPADLYAWMREFVKLLK 166
               SCOP domains d1g2ic_ C: Intracellular protease                                                                                                                                      SCOP domains
               CATH domains -1g2iC00 C:402-566  [code=3.40.50.880, no name defined]                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh.eeeeee...eeee.....eeee.ee.hhhhhhhh.eeee....hhhhhh.hhhhhhhhhhhhhh...eeee...hhhhhhhh.....ee..hhhhhhhhhhh..ee....eeee..eeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PEPTIDASE_C56_PFPI  PDB: C:401-566 UniProt: 1-166                                                                                                                      PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g2i C 401 mKVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFERGTITGKHGYSVKVDLTFDKVNPEEFDALVLPGGRAPERVRLNEKAVSIARKmFSEGKPVASICHGPQILISAGVLRGRKGTSYPGIKDDmINAGVEWVDAEVVVDGNWVSSRVPADLYAWmREFVKLLK 566
                            |      410       420       430       440       450       460       470       480       490       500       510       520      |530       540       550       560      
                          401-MSE                                                                                 489-MSE                               527-MSE                        558-MSE

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Flavodoxin-like (1057)

Superfamily: Class I glutamine amidotransferase-like (173)

Family: DJ-1/PfpI (54)

Protein domain: Intracellular protease (1)

Pyrococcus horikoshii [TaxId: 53953] (1)

1a	d1g2ia_	A:
1b	d1g2ib_	B:
1c	d1g2ic_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.880, no name defined] (97)

Pyrococcus horikoshii. Organism_taxid: 53953. (1)

1a	1g2iA00	A:2-166
1b	1g2iB00	B:202-366
1c	1g2iC00	C:402-566

(no "Pfam Domain" information available for 1G2I)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (PFPI_PYRHO | O59413)

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:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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