1Y23 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A MEMBER OF HIT FAMILY OF PROTEINS FROM BACILLUS SUBTILIS

Authors :   K. R. Rajashankar, C. D. Lima, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   19 Nov 04 (Deposition) - 07 Dec 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Hit Protein; Pkci-1; Cell-Cycle Regulation; Histidine Triad; Nysgxrc; Structural Genomics; Protein Structure Initiative; T2097; New York Sgx Research Center For Structural Genomics; Psi, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. R. Rajashankar, C. D. Lima
Crystal Structure Of A Member Of Hit Family Of Proteins From Bacillus Subtilis
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HISTIDINE TRIAD PROTEIN
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET T7
	Expression System Strain	:	B834, DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YHAE, HIT
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	HIT

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	ZN	5	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:7 , CYS A:10 , HIS A:49 , HIS A:100	BINDING SITE FOR RESIDUE ZN A 1001
2	AC2	SOFTWARE	CYS B:7 , CYS B:10 , HIS B:49 , HIS B:100	BINDING SITE FOR RESIDUE ZN B 1002
3	AC3	SOFTWARE	CYS C:7 , CYS C:10 , HIS C:49 , HIS C:100	BINDING SITE FOR RESIDUE ZN C 1003
4	AC4	SOFTWARE	CYS D:7 , CYS D:10 , HIS D:49 , HIS D:100	BINDING SITE FOR RESIDUE ZN D 1004
5	AC5	SOFTWARE	CYS E:7 , CYS E:10 , HIS E:49 , HIS E:100	BINDING SITE FOR RESIDUE ZN E 1005
6	AC6	SOFTWARE	ARG B:141 , SER B:144 , HOH B:2023 , HOH B:2035 , HOH B:2036 , ASP E:125	BINDING SITE FOR RESIDUE MG B 2001

(no "SS Bond" information available for 1Y23)

(no "Cis Peptide Bond" information available for 1Y23)

(no "SAP(SNP)/Variant" information available for 1Y23)

Asymmetric Unit (2, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIT_2	PS51084	HIT domain profile.	HIT_BACSU	8-116	5	A:8-116 B:8-116 C:8-116 D:8-116 E:8-116
2	HIT_1	PS00892	HIT domain signature.	HIT_BACSU	89-107	5	A:89-107 B:89-107 C:89-107 D:89-107 E:89-107

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIT_2	PS51084	HIT domain profile.	HIT_BACSU	8-116	2	A:8-116 B:8-116 - - -
2	HIT_1	PS00892	HIT domain signature.	HIT_BACSU	89-107	2	A:89-107 B:89-107 - - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIT_2	PS51084	HIT domain profile.	HIT_BACSU	8-116	2	- - C:8-116 D:8-116 -
2	HIT_1	PS00892	HIT domain signature.	HIT_BACSU	89-107	2	- - C:89-107 D:89-107 -

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIT_2	PS51084	HIT domain profile.	HIT_BACSU	8-116	2	- - - - E:8-116
2	HIT_1	PS00892	HIT domain signature.	HIT_BACSU	89-107	2	- - - - E:89-107

(no "Exon" information available for 1Y23)

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:139
 aligned with HIT_BACSU | O07513 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:139
                                    14        24        34        44        54        64        74        84        94       104       114       124       134         
            HIT_BACSU     5 ENCIFCKIIAGDIPSAKVYEDEHVLAFLDISQVTKGHTLVIPKTHIENVYEFTDELAKQYFHAVPKIARAIRDEFEPIGLNTLNNNGEKAGQSVFHYHMHIIPRYGKGDGFGAVWKTHADDYKPEDLQNISSSIAKRLA 143
               SCOP domains d1y23a_ A: Hit                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh......eeee...eeeee.........eeeee.....hhhhhhhhhhhh..hhhhhhhhhhhhhhh..eeeeeeeehhhhh.......eeeeee......eeeee..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---HIT_2  PDB: A:8-116 UniProt: 8-116                                                                           --------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------HIT_1  PDB: A:89-10------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y23 A   5 ENCIFCKIIAGDIPSAKVYEDEHVLAFLDISQVTKGHTLVIPKTHIENVYEFTDELAKQYFHAVPKIARAIRDEFEPIGLNTLNNNGEKAGQSVFHYHMHIIPRYGKGDGFGAVWKTHADDYKPEDLQNISSSIAKRLA 143
                                    14        24        34        44        54        64        74        84        94       104       114       124       134

Chain B from PDB  Type:PROTEIN  Length:141
 aligned with HIT_BACSU | O07513 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:141
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144 
            HIT_BACSU     5 ENCIFCKIIAGDIPSAKVYEDEHVLAFLDISQVTKGHTLVIPKTHIENVYEFTDELAKQYFHAVPKIARAIRDEFEPIGLNTLNNNGEKAGQSVFHYHMHIIPRYGKGDGFGAVWKTHADDYKPEDLQNISSSIAKRLASS 145
               SCOP domains d1y23b_ B: Hit                                                                                                                                SCOP domains
               CATH domains 1y23B01 B:5-116 HIT family, subunit A                                                                           ----------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh......eeee...eeeee.........eeeee.....hhhhhhhhhhhh..hhhhhhhhhhhhhhh..eeeeeeeehhhhh.......eeeeee......eeeee..hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---HIT_2  PDB: B:8-116 UniProt: 8-116                                                                           ----------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------HIT_1  PDB: B:89-10-------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y23 B   5 ENCIFCKIIAGDIPSAKVYEDEHVLAFLDISQVTKGHTLVIPKTHIENVYEFTDELAKQYFHAVPKIARAIRDEFEPIGLNTLNNNGEKAGQSVFHYHMHIIPRYGKGDGFGAVWKTHADDYKPEDLQNISSSIAKRLASS 145
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144

Chain C from PDB  Type:PROTEIN  Length:138
 aligned with HIT_BACSU | O07513 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:138
                                    14        24        34        44        54        64        74        84        94       104       114       124       134        
            HIT_BACSU     5 ENCIFCKIIAGDIPSAKVYEDEHVLAFLDISQVTKGHTLVIPKTHIENVYEFTDELAKQYFHAVPKIARAIRDEFEPIGLNTLNNNGEKAGQSVFHYHMHIIPRYGKGDGFGAVWKTHADDYKPEDLQNISSSIAKRL 142
               SCOP domains d1y23c_ C: Hit                                                                                                                             SCOP domains
               CATH domains 1y23C01 C:5-116 HIT family, subunit A                                                                           -------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhh.....eeee...eeeee.........eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhh.......eeeeee......eeeee..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---HIT_2  PDB: C:8-116 UniProt: 8-116                                                                           -------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------HIT_1  PDB: C:89-10----------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y23 C   5 ENCIFCKIIAGDIPSAKVYEDEHVLAFLDISQVTKGHTLVIPKTHIENVYEFTDELAKQYFHAVPKIARAIRDEFEPIGLNTLNNNGEKAGQSVFHYHMHIIPRYGKGDGFGAVWKTHADDYKPEDLQNISSSIAKRL 142
                                    14        24        34        44        54        64        74        84        94       104       114       124       134

Chain D from PDB  Type:PROTEIN  Length:139
 aligned with HIT_BACSU | O07513 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:139
                                    14        24        34        44        54        64        74        84        94       104       114       124       134         
            HIT_BACSU     5 ENCIFCKIIAGDIPSAKVYEDEHVLAFLDISQVTKGHTLVIPKTHIENVYEFTDELAKQYFHAVPKIARAIRDEFEPIGLNTLNNNGEKAGQSVFHYHMHIIPRYGKGDGFGAVWKTHADDYKPEDLQNISSSIAKRLA 143
               SCOP domains d1y23d_ D: Hit                                                                                                                              SCOP domains
               CATH domains 1y23D01 D:5-116 HIT family, subunit A                                                                           --------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.....eeee...eeeee.........eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhh.......eeeeee......eeeee..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---HIT_2  PDB: D:8-116 UniProt: 8-116                                                                           --------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------HIT_1  PDB: D:89-10------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y23 D   5 ENCIFCKIIAGDIPSAKVYEDEHVLAFLDISQVTKGHTLVIPKTHIENVYEFTDELAKQYFHAVPKIARAIRDEFEPIGLNTLNNNGEKAGQSVFHYHMHIIPRYGKGDGFGAVWKTHADDYKPEDLQNISSSIAKRLA 143
                                    14        24        34        44        54        64        74        84        94       104       114       124       134

Chain E from PDB  Type:PROTEIN  Length:141
 aligned with HIT_BACSU | O07513 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:141
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144 
            HIT_BACSU     5 ENCIFCKIIAGDIPSAKVYEDEHVLAFLDISQVTKGHTLVIPKTHIENVYEFTDELAKQYFHAVPKIARAIRDEFEPIGLNTLNNNGEKAGQSVFHYHMHIIPRYGKGDGFGAVWKTHADDYKPEDLQNISSSIAKRLASS 145
               SCOP domains d1y23e_ E: Hit                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------HIT-1y23E01 E:14-111                                                                              ---------------------------------- Pfam domains (1)
           Pfam domains (2) ---------HIT-1y23E02 E:14-111                                                                              ---------------------------------- Pfam domains (2)
           Pfam domains (3) ---------HIT-1y23E03 E:14-111                                                                              ---------------------------------- Pfam domains (3)
           Pfam domains (4) ---------HIT-1y23E04 E:14-111                                                                              ---------------------------------- Pfam domains (4)
           Pfam domains (5) ---------HIT-1y23E05 E:14-111                                                                              ---------------------------------- Pfam domains (5)
         Sec.struct. author ..hhhhhhhh......eeee...eeeee.........eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhh.......eeeeee.............hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---HIT_2  PDB: E:8-116 UniProt: 8-116                                                                           ----------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------HIT_1  PDB: E:89-10-------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y23 E   5 ENCIFCKIIAGDIPSAKVYEDEHVLAFLDISQVTKGHTLVIPKTHIENVYEFTDELAKQYFHAVPKIARAIRDEFEPIGLNTLNNNGEKAGQSVFHYHMHIIPRYGKGDGFGAVWKTHADDYKPEDLQNISSSIAKRLASS 145
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144

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) (23004)

Fold: HIT-like (73)

Superfamily: HIT-like (67)

Family: HIT (HINT, histidine triad) family of protein kinase-interacting proteins (38)

Protein domain: Hit (1)

Bacillus subtilis [TaxId: 1423] (1)

1a	d1y23a_	A:
1b	d1y23b_	B:
1c	d1y23c_	C:
1d	d1y23d_	D:
1e	d1y23e_	E:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: HIT family, subunit A (33)

Homologous Superfamily: HIT family, subunit A (27)

Bacillus subtilis. Organism_taxid: 1423. (1)

1a	1y23B01	B:5-116
1b	1y23C01	C:5-116
1c	1y23D01	D:5-116

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HIT (23)

Family: HIT (19)

Bacillus subtilis (1)

1a	HIT-1y23E01	E:14-111
1b	HIT-1y23E02	E:14-111
1c	HIT-1y23E03	E:14-111
1d	HIT-1y23E04	E:14-111
1e	HIT-1y23E05	E:14-111

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (HIT_BACSU | O07513)

molecular function
	GO:0003824		catalytic activity		Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

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	1y23
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Description

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Ligands, Modified Residues, Ions (2, 6)

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