1OKJ - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE ESSENTIAL E. COLI YEAZ PROTEIN BY MAD METHOD USING THE GADOLINIUM COMPLEX "DOTMA"

Authors :   C. Abergel, S. Jeudy, J. M. Claverie

Date :   26 Jul 03 (Deposition) - 16 Sep 04 (Release) - 23 Jul 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.28

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

Keywords :   Potential Zinc Protease, Hypothetical Protease Yeaz, Metalloprotease, Hydrolase, Bacterial Targets At Igs-Cnrs, France, Bigs, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Stelter, R. Molina, S. Jeudy, R. Kahn, C. Abergel, J. A. Hermoso
A Complement To The Modern Crystallographer'S Toolbox: Caged Gadolinium Complexes With Versatile Binding Modes.
Acta Crystallogr. , Sect. D V. 70 1506 2014
PubMed-ID: 24914962 | Reference-DOI: 10.1107/S1399004714005483
(for further references see the PDB file header)

Molecule 1 - TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB
	Chains	:	A, B, C, D
	EC Number	:	3.4.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST17
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Other Details	:	GATEWAY PEPTIDE INSERTED ON THE PROTEIN SEQUENCE FOR PROTEIN EXPRESSION AND PURIFICATION
	Strain	:	K-12
	Synonym	:	HYPOTHETICAL PROTEASE YEAZ, T(6)A37 THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN TSAB

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	GD3	8	Ligand/Ion	GADOLINIUM ION

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	GD3	8	Ligand/Ion	GADOLINIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	GD3	-1	Ligand/Ion	GADOLINIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH B:2029	BINDING SITE FOR RESIDUE GD3 A1214
2	AC2	SOFTWARE	ARG B:31	BINDING SITE FOR RESIDUE GD3 A1216
3	AC3	SOFTWARE	ARG A:31	BINDING SITE FOR RESIDUE GD3 A1218

Asymmetric Unit

No.	Residues
1	A:12	-	A:29
2	B:12	-	B:29
3	C:12	-	C:29

Asymmetric Unit

No.	Residues
1	Gly A:63	-	Pro A:64
2	Gly B:63	-	Pro B:64
3	Gly C:63	-	Pro C:64
4	Gly D:63	-	Pro D:64

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

(no "PROSITE Motif" information available for 1OKJ)

(no "Exon" information available for 1OKJ)

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:220
 aligned with TSAB_ECOLI | P76256 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:220
                             1                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219
           TSAB_ECOLI     - -MRILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQGAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVHERMQQLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAAEDMLPIACQMFAEGKTVAVEHAEPVYLR 219
               SCOP domains --d1okja1 A:1-106 Hypothetical protein YeaZ                                                                 d1okja2 A:107-216 Hypothetical protein YeaZ                                                                   -- SCOP domains
               CATH domains 1okjA01 A:-1-92,A:188-218  [code=3.30.420.40, no name defined]                                1okjA02 A:93-187  [code=3.30.420.40, no name defined]                                          1okjA01 A:-1-92,A:188-218       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeeee..eeeeeeee.......hhhhhhhhhhhhh..hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhh...eeeeeee.....eeeeeeee.....eehhhhheeehhhhhhhhhh....eeeeehhhhhhh.........eeee......hhhhhhhhhhhhhhhh...hhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1okj A  -1 GLRILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQGAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVHERMQQLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAAEDMLPIACQMFAEGKTVAVEHAEPVYLR 218
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218

Chain B from PDB  Type:PROTEIN  Length:223
 aligned with TSAB_ECOLI | P76256 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:223
                                1                                                                                                                                                                                                                          
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216   
           TSAB_ECOLI     - ----MRILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQGAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVHERMQQLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAAEDMLPIACQMFAEGKTVAVEHAEPVYLR 219
               SCOP domains -----d1okjb1 B:1-106 Hypothetical protein YeaZ                                                                 d1okjb2 B:107-216 Hypothetical protein YeaZ                                                                   -- SCOP domains
               CATH domains 1okjB01 B:-4-92,B:188-218  [code=3.30.420.40, no name defined]                                   1okjB02 B:93-187  [code=3.30.420.40, no name defined]                                          1okjB01 B:-4-92,B:188-218       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee....eeeeeeee..eeeeeeee.hhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeee.....eehhhhheeehhhhhhhhhh....eeeee.hhhhhhhhhh.....eeee......hhhhhhhhhhhhhhh....hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1okj B  -4 KKAGLRILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQGAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVHERMQQLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAAEDMLPIACQMFAEGKTVAVEHAEPVYLR 218
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215

Chain C from PDB  Type:PROTEIN  Length:219
 aligned with TSAB_ECOLI | P76256 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:219
                             1                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209         
           TSAB_ECOLI     - -MRILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQGAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVHERMQQLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAAEDMLPIACQMFAEGKTVAVEHAEPVYL 218
               SCOP domains --d1okjc1 C:1-106 Hypothetical protein YeaZ                                                                 d1okjc2 C:107-216 Hypothetical protein YeaZ                                                                   - SCOP domains
               CATH domains 1okjC01 C:-1-92,C:188-217  [code=3.30.420.40, no name defined]                                1okjC02 C:93-187  [code=3.30.420.40, no name defined]                                          1okjC01 C:-1-92,C:188-217      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeeee...eeeeeee.hhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhh..eeeeeee.....eeeeeeee.....eehhhhheeehhhhhhhhhh....eeeeehhhhhhhhhhh.....eeee......hhhhhhhhhhhhhhh....hhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1okj C  -1 GLRILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQGAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVHERMQQLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAAEDMLPIACQMFAEGKTVAVEHAEPVYL 217
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

Chain D from PDB  Type:PROTEIN  Length:221
 aligned with TSAB_ECOLI | P76256 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:221
                              1                                                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218 
           TSAB_ECOLI     - --MRILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQGAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVHERMQQLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAAEDMLPIACQMFAEGKTVAVEHAEPVYLR 219
               SCOP domains ---d1okjd1 D:1-106 Hypothetical protein YeaZ                                                                 d1okjd2 D:107-216 Hypothetical protein YeaZ                                                                   -- SCOP domains
               CATH domains 1okjD01 D:-2-92,D:188-218  [code=3.30.420.40, no name defined]                                 1okjD02 D:93-187  [code=3.30.420.40, no name defined]                                          1okjD01 D:-2-92,D:188-218       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhh.hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhh..eeeeeee.....eeeeeeee.....eehhhhheeehhhhhhhhhh....eeeee.hhhhhh.........eeee......hhhhhhhhhhhhhhh....hhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1okj D  -2 AGLRILAIDTATEACSVALWNDGTVNAHFELCPREHTQRILPMVQDILTTSGTSLTDINALAYGRGPGSFTGVRIGIGIAQGLALGAELPMIGVSTLMTMAQGAWRKNGATRVLAAIDARMGEVYWAEYQRDENGIWHGEETEAVLKPEIVHERMQQLSGEWVTVGTGWQAWPDLGKESGLVLRDGEVLLPAAEDMLPIACQMFAEGKTVAVEHAEPVYLR 218
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217

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) (23833)

Fold: Ribonuclease H-like motif (1424)

Superfamily: Actin-like ATPase domain (426)

Family: YeaZ-like (2)

Protein domain: Hypothetical protein YeaZ (1)

Escherichia coli [TaxId: 562] (1)

1a	d1okja1	A:1-106
1b	d1okja2	A:107-216
1c	d1okjb1	B:1-106
1d	d1okjb2	B:107-216
1e	d1okjc1	C:1-106
1f	d1okjc2	C:107-216
1g	d1okjd1	D:1-106
1h	d1okjd2	D:107-216

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Nucleotidyltransferase; domain 5 (788)

Homologous Superfamily: [code=3.30.420.40, no name defined] (217)

Escherichia coli. Organism_taxid: 83333. Strain: k12. (1)

1a	1okjB01	B:-4-92,B:188-218
1b	1okjD01	D:-2-92,D:188-218
1c	1okjA01	A:-1-92,A:188-218
1d	1okjC01	C:-1-92,C:188-217
1e	1okjA02	A:93-187
1f	1okjB02	B:93-187
1g	1okjC02	C:93-187
1h	1okjD02	D:93-187

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TSAB_ECOLI | P76256)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
	GO:0002949	tRNA threonylcarbamoyladenosine modification	The attachment of a carbonyl group and a threonine to the amino group of the adenine residue immediately 3' of the anticodon, in tRNAs that decode ANN codons (where N is any base).
cellular component
	GO:0000408	EKC/KEOPS complex	A protein complex involved in t6A tRNA modification; originally proposed to be involved in transcription as well as promoting telomere uncapping and telomere elongation. For example, in Saccharomyces cerevisiae the complex contains Bud32p, Kae1p, Gon7p, Cgi121p, and Pcc1p.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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		Gly D:63 - Pro D:64	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 1OKJ)

Description

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