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Title :   2.1A CRYSTAL STRUCTURE OF SALMONELLA TYHPIMURIUM YEAZ, A PUTATIVE GRAM-NEGATIVE RPF, FORM-A

Authors :   C. E. Nichols, D. K. Stammers

Date :   20 Mar 06 (Deposition) - 01 Aug 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   M22, Glycoprotease, Yeaz, Actin-Like-Fold, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. E. Nichols, C. Johnson, M. Lockyer, I. G. Charles, H. K. Lamb, A. R. Hawkins, D. K. Stammers
Structural Characterization Of Salmonella Typhimurium Yeaz, An M22 O-Sialoglycoprotein Endopeptidase Homolog
Proteins V. 64 111 2006
PubMed-ID: 16617437 | Reference-DOI: 10.1002/PROT.20982
(for further references see the PDB file header)

Molecule 1 - PUTATIVE GRAM NEGATIVE RESUSCITATION PROMOTING FACTOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PMUT101
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PET3D
	Gene	:	YEGS,YEAZ
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	602
	Strain	:	SL3261

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2GEM)

(no "Site" information available for 2GEM)

Asymmetric Unit

No.	Residues
1	A:13	-	A:30
2	B:13	-	B:30

Asymmetric Unit

No.	Residues
1	Gly A:64	-	Pro A:65
2	Gly B:64	-	Pro B:65

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

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

(no "Exon" information available for 2GEM)

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:216
 aligned with TSAB_SALTY | Q7CQE0 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
           TSAB_SALTY     1 MRILAIDTATEACSVALWNNGTINAHFELCPREHTQRILPMVQEILAASGASLNEIDALAFGRGPGSFTGVRIGIGIAQGLALGANLPMIGVSTLATMAQGAWRKTGATRVLAAIDARMGEVYWAEYQRDAQGVWQGEETEAVLKPERVGERLKQLSGEWATVGTGWSAWPDLAKECGLTLHDGEVSLPAAEDMLPIASQKLAAGETVAVEHAEPVYL 218
               SCOP domains d2gema1 A:1-107 automated matc  hes                                                                        d2gema2 A:108-218 automated matches                                                                             SCOP domains
               CATH domains 2gemA01 A:1-93,A:189-218  [cod  e=3.30.420.40, no name defined]                              2gemA02 A:94-188  [code=3.30.420.40, no name defined]                                          2gemA01 A:1-93,A:189-218       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeeee..eeeeeeee.--....hhhhhhhhhhhhh........eeeee....hhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh..eeeeeeee...eeeeeeeee.....eehhhhheeehhhhhhhhhh....eeeee.hhhhhh.hhhhhh..eeeeeee...hhhhhhhhhhhhhhh....hhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gem A   1 MRILAIDTATEACSVALWNNGTINAHFELC--EHTQRILPMVQEILAASGASLNEIDALAFGRGPGSFTGVRIGIGIAQGLALGANLPMIGVSTLATMAQGAWRKTGATRVLAAIDARMGEVYWAEYQRDAQGVWQGEETEAVLKPERVGERLKQLSGEWATVGTGWSAWPDLAKECGLTLHDGEVSLPAAEDMLPIASQKLAAGETVAVEHAEPVYL 218
                                    10        20        30  |     40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
                                                        30 33

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with TSAB_SALTY | Q7CQE0 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
           TSAB_SALTY     1 MRILAIDTATEACSVALWNNGTINAHFELCPREHTQRILPMVQEILAASGASLNEIDALAFGRGPGSFTGVRIGIGIAQGLALGANLPMIGVSTLATMAQGAWRKTGATRVLAAIDARMGEVYWAEYQRDAQGVWQGEETEAVLKPERVGERLKQLSGEWATVGTGWSAWPDLAKECGLTLHDGEVSLPAAEDMLPIASQKLAAGETVAVEHAEPVYL 218
               SCOP domains d2gemb1 B:1-107 automated matc  hes                                                                        d2gemb2 B:108-218 automated matches                                                                             SCOP domains
               CATH domains 2gemB01 B:1-93,B:189-218  [cod  e=3.30.420.40, no name defined]                              2gemB02 B:94-188  [code=3.30.420.40, no name defined]                                          2gemB01 B:1-93,B:189-218       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeeee..eeeeeeee.--.hhhhhhhhhhhhhhhh........eeeeeee..hhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhh...eeeeeeee...eeeeeeeee.....eehhhhheeehhhhhhhhhh....eeeee.hhhhhh.........eeeeeee...hhhhhhhhhhhhhhh....hhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gem B   1 MRILAIDTATEACSVALWNNGTINAHFELC--EHTQRILPMVQEILAASGASLNEIDALAFGRGPGSFTGVRIGIGIAQGLALGANLPMIGVSTLATMAQGAWRKTGATRVLAAIDARMGEVYWAEYQRDAQGVWQGEETEAVLKPERVGERLKQLSGEWATVGTGWSAWPDLAKECGLTLHDGEVSLPAAEDMLPIASQKLAAGETVAVEHAEPVYL 218
                                    10        20        30  |     40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
                                                        30 33

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: automated matches (111)

Protein domain: automated matches (111)

Salmonella typhimurium [TaxId: 602] (1)

1a	d2gema1	A:1-107
1b	d2gema2	A:108-218
1c	d2gemb1	B:1-107
1d	d2gemb2	B:108-218

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)

Salmonella typhimurium. Organism_taxid: 602. Strain: sl3261. (1)

1a	2gemA01	A:1-93,A:189-218
1b	2gemB01	B:1-93,B:189-218
1c	2gemA02	A:94-188
1d	2gemB02	B:94-188

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (TSAB_SALTY | Q7CQE0)

biological process
	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.

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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2gem)

	Sites
(no "Sites" information available for 2gem)

	Cis Peptide Bonds
		Gly A:64 - Pro A:65	[ RasMol ]
		Gly B:64 - Pro B:65	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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2gel	2.05A STRUCTURE OF SALMONELLA TYPHIMURIUM YEAZ, A PUTATIVE GRAM-NEGATIVE RPF, FORM-B

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 4)

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