2I52 - JenaLib

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Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PROTEIN PTO0218 FROM PICROPHILUS TORRIDUS, PFAM DUF372

Authors :   U. A. Ramagopal, J. Gilmore, R. Toro, K. T. Bain, C. Mckenzie, C. Reyes, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center Structural Genomics (Nysgxrc)

Date :   23 Aug 06 (Deposition) - 12 Sep 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.08

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: E,F  (2x)
Biol. Unit 3: A,B,C,D,E,F  (2x)
Biol. Unit 4: A (2x),B (2x),C (2x),D (2x),E (2x),F (2x)

Keywords :   Structural Genomics, Unknown Function, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. A. Ramagopal, J. Gilmore, R. Toro, K. T. Bain, C. Mckenzie, C. Reyes, J. M. Sauder, S. K. Burley, S. C. Almo
Structure Of Hypothetical Protein Pto0218 From Picrophilus Torridus
To Be Published
PubMed: search

Molecule 1 - HYPOTHETICAL PROTEIN
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BS-PSGX4(BS)
	Expression System Strain	:	BL21(DE3)-CODON+RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PICROPHILUS TORRIDUS
	Organism Taxid	:	263820
	Strain	:	DSM 9790

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (2x)	:					E	F
Biological Unit 3 (2x)	:	A	B	C	D	E	F
Biological Unit 4 (2x)	:	A (2x)	B (2x)	C (2x)	D (2x)	E (2x)	F (2x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 17)

No.	Name	Count	Type	Full Name
1	CA	12	Ligand/Ion	CALCIUM ION
2	CL	1	Ligand/Ion	CHLORIDE ION
3	GOL	4	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	3	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 3 (1, 8)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	8	Ligand/Ion	GLYCEROL

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	-1	Ligand/Ion	GLYCEROL

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU B:46 , HOH B:818 , HOH B:842 , GLU F:46 , HOH F:908 , HOH F:933	BINDING SITE FOR RESIDUE CA B 801
02	AC2	SOFTWARE	HOH A:838 , HIS B:30 , THR B:33 , HOH B:824 , HIS C:30 , THR C:33 , HOH D:911	BINDING SITE FOR RESIDUE CA B 802
03	AC3	SOFTWARE	GLU C:46 , SER C:65 , HOH C:812 , HOH C:819 , HOH C:861 , HOH C:869	BINDING SITE FOR RESIDUE CA C 803
04	AC4	SOFTWARE	GLU D:50 , HOH D:915 , HOH D:925 , HOH D:948 , HOH D:964 , HOH D:974	BINDING SITE FOR RESIDUE CA D 804
05	AC5	SOFTWARE	SER A:65 , GLU E:46 , CA E:806 , HOH E:834 , HOH E:843 , HOH E:851 , HOH E:898 , HOH E:926	BINDING SITE FOR RESIDUE CA E 805
06	AC6	SOFTWARE	SER A:65 , SER E:65 , CA E:805 , HOH E:830 , HOH E:843 , HOH E:851 , HOH E:853	BINDING SITE FOR RESIDUE CA E 806
07	AC7	SOFTWARE	THR A:33 , HOH A:907 , HOH B:898 , HOH C:907 , THR D:33 , HOH D:905 , HOH D:930	BINDING SITE FOR RESIDUE CA A 807
08	AC8	SOFTWARE	HOH E:868 , HIS F:30 , THR F:33 , HOH F:905 , HOH F:967	BINDING SITE FOR RESIDUE CA F 808
09	AC9	SOFTWARE	HIS E:30 , THR E:33 , HOH E:813 , HOH F:922	BINDING SITE FOR RESIDUE CA E 809
10	BC1	SOFTWARE	MET B:54 , HOH B:851 , HOH B:860 , HOH D:904 , HOH D:993	BINDING SITE FOR RESIDUE CA B 810
11	BC2	SOFTWARE	ASN C:61 , HOH C:843 , HOH C:844 , HOH C:854 , HOH C:898	BINDING SITE FOR RESIDUE CA C 811
12	BC3	SOFTWARE	GLU A:46 , HOH A:815 , HOH A:906 , SER E:65 , HOH E:830 , HOH E:853	BINDING SITE FOR RESIDUE CA E 812
13	BC4	SOFTWARE	ASP B:13 , ILE B:14	BINDING SITE FOR RESIDUE CL B 813
14	BC5	SOFTWARE	TYR B:78 , HOH B:832 , PHE C:29 , HIS C:30 , GLN D:56 , HOH D:913 , HOH D:938	BINDING SITE FOR RESIDUE GOL D 901
15	BC6	SOFTWARE	TYR A:78 , SER A:80 , GLN C:56 , PHE D:29 , HIS D:30 , TYR D:111 , PRO D:112 , HOH D:910 , HOH D:914 , HOH D:933	BINDING SITE FOR RESIDUE GOL D 902
16	BC7	SOFTWARE	GLU D:89 , LEU D:100 , VAL D:102 , TYR D:115 , HOH D:975	BINDING SITE FOR RESIDUE GOL D 903
17	BC8	SOFTWARE	SER B:43 , GLU B:47 , HOH B:889 , GLU F:47 , GLU F:50 , ARG F:51 , HOH F:914 , HOH F:927	BINDING SITE FOR RESIDUE GOL F 904

(no "SS Bond" information available for 2I52)

(no "Cis Peptide Bond" information available for 2I52)

(no "SAP(SNP)/Variant" information available for 2I52)

(no "PROSITE Motif" information available for 2I52)

(no "Exon" information available for 2I52)

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:115
 aligned with MPTD_PICTO | Q6L2J9 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:121
                             1                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119 
           MPTD_PICTO     - -MYDPAEKYFNCTDIQRAFFEAGIKLGAIFHQYTGIPVNSENASMAEEFIERSTMIQPFVENVRISINNVKRSSGTYSYSSLNEKMLHAEVLINYNGKKVLGVLNYDEGLDYPVMYAKEVL 120
               SCOP domains -d2i52a1 A:1-120 Hypothetical protein PTO0218                                                                             SCOP domains
               CATH domains 2i52A00 A:0-120 MK0786-like domain                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..hhhhhhhhhhhhhhhhhhhhhh..ee...hhhhhhhhhhhhhh....eeeeeeee...------...ee.....eeeeeeeee..eeeeeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i52 A   0 SLYDPAEKYFNCTDIQRAFFEAGIKLGAIFHQYTGIPVNSENASMAEEFIERSTMIQPFVENVRISINNV------YSYSSLNEKMLHAEVLINYNGKKVLGVLNYDEGLDYPVMYAKEVL 120
                                     9        19        29        39        49        59        69      | 79        89        99       109       119 
                                                                                                69     76

Chain B from PDB  Type:PROTEIN  Length:116
 aligned with MPTD_PICTO | Q6L2J9 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:121
                             1                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119 
           MPTD_PICTO     - -MYDPAEKYFNCTDIQRAFFEAGIKLGAIFHQYTGIPVNSENASMAEEFIERSTMIQPFVENVRISINNVKRSSGTYSYSSLNEKMLHAEVLINYNGKKVLGVLNYDEGLDYPVMYAKEVL 120
               SCOP domains d2i52b_ B: Hypothetical protein PTO0218                                                                                   SCOP domains
               CATH domains 2i52B00 B:0-120 MK0786-like domain                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..hhhhhhhhhhhhhhhhhhhhhh..ee...hhhhhhhhhhhhhhh...eeeeeeee....-----...ee.....eeeeeeeee..eeeeeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i52 B   0 SLYDPAEKYFNCTDIQRAFFEAGIKLGAIFHQYTGIPVNSENASMAEEFIERSTMIQPFVENVRISINNVK-----YSYSSLNEKMLHAEVLINYNGKKVLGVLNYDEGLDYPVMYAKEVL 120
                                     9        19        29        39        49        59        69|     | 79        89        99       109       119 
                                                                                                 70    76

Chain C from PDB  Type:PROTEIN  Length:115
 aligned with MPTD_PICTO | Q6L2J9 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:121
                             1                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119 
           MPTD_PICTO     - -MYDPAEKYFNCTDIQRAFFEAGIKLGAIFHQYTGIPVNSENASMAEEFIERSTMIQPFVENVRISINNVKRSSGTYSYSSLNEKMLHAEVLINYNGKKVLGVLNYDEGLDYPVMYAKEVL 120
               SCOP domains d2i52c_ C: Hypothetical protein PTO0218                                                                                   SCOP domains
               CATH domains 2i52C00 C:0-120 MK0786-like domain                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..hhhhhhhhhhhhhhhhhhhhhh..ee...hhhhhhhhhhhhhhh...eeeeeeee...------...ee.....eeeeeeeee..eeeeeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i52 C   0 SLYDPAEKYFNCTDIQRAFFEAGIKLGAIFHQYTGIPVNSENASMAEEFIERSTMIQPFVENVRISINNV------YSYSSLNEKMLHAEVLINYNGKKVLGVLNYDEGLDYPVMYAKEVL 120
                                     9        19        29        39        49        59        69      | 79        89        99       109       119 
                                                                                                69     76

Chain D from PDB  Type:PROTEIN  Length:117
 aligned with MPTD_PICTO | Q6L2J9 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:121
                             1                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119 
           MPTD_PICTO     - -MYDPAEKYFNCTDIQRAFFEAGIKLGAIFHQYTGIPVNSENASMAEEFIERSTMIQPFVENVRISINNVKRSSGTYSYSSLNEKMLHAEVLINYNGKKVLGVLNYDEGLDYPVMYAKEVL 120
               SCOP domains d2i52d_ D: Hypothetical protein PTO0218                                                                                   SCOP domains
               CATH domains 2i52D00 D:0-120 MK0786-like domain                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..hhhhhhhhhhhhhhhhhhhhhh..ee...hhhhhhhhhhhhhhh...eeeeeeee..----......ee.....eeeeeeeee..eeeeeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i52 D   0 SLYDPAEKYFNCTDIQRAFFEAGIKLGAIFHQYTGIPVNSENASMAEEFIERSTMIQPFVENVRISINN----SGTYSYSSLNEKMLHAEVLINYNGKKVLGVLNYDEGLDYPVMYAKEVL 120
                                     9        19        29        39        49        59        |-   |    79        89        99       109       119 
                                                                                               68   73

Chain E from PDB  Type:PROTEIN  Length:115
 aligned with MPTD_PICTO | Q6L2J9 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:121
                             1                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119 
           MPTD_PICTO     - -MYDPAEKYFNCTDIQRAFFEAGIKLGAIFHQYTGIPVNSENASMAEEFIERSTMIQPFVENVRISINNVKRSSGTYSYSSLNEKMLHAEVLINYNGKKVLGVLNYDEGLDYPVMYAKEVL 120
               SCOP domains d2i52e_ E: Hypothetical protein PTO0218                                                                                   SCOP domains
               CATH domains 2i52E00 E:0-120 MK0786-like domain                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..hhhhhhhhhhhhhhhhhhhhhh..ee...hhhhhhhhhhhhhhh...eeeeeeee...------...ee.....eeeeeeeee..eeeeeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i52 E   0 SLYDPAEKYFNCTDIQRAFFEAGIKLGAIFHQYTGIPVNSENASMAEEFIERSTMIQPFVENVRISINNV------YSYSSLNEKMLHAEVLINYNGKKVLGVLNYDEGLDYPVMYAKEVL 120
                                     9        19        29        39        49        59        69      | 79        89        99       109       119 
                                                                                                69     76

Chain F from PDB  Type:PROTEIN  Length:119
 aligned with MPTD_PICTO | Q6L2J9 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:121
                             1                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119 
           MPTD_PICTO     - -MYDPAEKYFNCTDIQRAFFEAGIKLGAIFHQYTGIPVNSENASMAEEFIERSTMIQPFVENVRISINNVKRSSGTYSYSSLNEKMLHAEVLINYNGKKVLGVLNYDEGLDYPVMYAKEVL 120
               SCOP domains d2i52f_ F: Hypothetical protein PTO0218                                                                                   SCOP domains
               CATH domains 2i52F00 F:0-120 MK0786-like domain                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..hhhhhhhhhhhhhhhhhhhhhh..ee...hhhhhhhhhhhhhhh...eeeeeeee......--....ee.....eeeeeeeee..eeeeeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i52 F   0 SLYDPAEKYFNCTDIQRAFFEAGIKLGAIFHQYTGIPVNSENASMAEEFIERSTMIQPFVENVRISINNVKRS--TYSYSSLNEKMLHAEVLINYNGKKVLGVLNYDEGLDYPVMYAKEVL 120
                                     9        19        29        39        49        59        69  |  |  79        89        99       109       119 
                                                                                                   72 75

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: Alpha and beta proteins (a+b) (23004)

Fold: MK0786-like (3)

Superfamily: MK0786-like (3)

Family: MK0786-like (2)

Protein domain: Hypothetical protein PTO0218 (1)

Picrophilus torridus [TaxId: 82076] (1)

1a	d2i52a1	A:1-120
1b	d2i52b_	B:
1c	d2i52c_	C:
1d	d2i52d_	D:
1e	d2i52e_	E:
1f	d2i52f_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Pantoate--beta-alanine Ligase; Chain: A,domain 2 (43)

Homologous Superfamily: MK0786-like domain (3)

Picrophilus torridus dsm 9790. Organism_taxid: 263820. Strain: dsm 9790. (1)

1a	2i52B00	B:0-120
1b	2i52D00	D:0-120
1c	2i52A00	A:0-120
1d	2i52C00	C:0-120
1e	2i52E00	E:0-120
1f	2i52F00	F:0-120

(no "Pfam Domain" information available for 2I52)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (MPTD_PICTO | Q6L2J9)

molecular function
	GO:0004150		dihydroneopterin aldolase activity		Catalysis of the reaction: 2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8-dihydropteridine = 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine + glycolaldehyde.
	GO:0016829		lyase activity		Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.

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Description

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Ligands, Modified Residues, Ions (3, 17)

Sites (17, 17)

SS Bonds (0, 0)

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