3ZEU - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF A SALMONELLA TYPHIMURIUM YGJD-YEAZ HETERODIMER BOUND TO ATPGAMMAS

Authors :   C. E. Nichols, H. K. Lamb, P. Thompson, K. El Omari, M. Lockyer, I. Charl A. R. Hawkins, D. K. Stammers

Date :   07 Dec 12 (Deposition) - 20 Mar 13 (Release) - 29 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Hydrolase, Nucleotide Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. E. Nichols, H. K. Lamb, P. Thompson, K. E. Omari, M. Lockyer, I. Charles, A. R. Hawkins, D. K. Stammers
Crystal Structure Of The Dimer Of Two Essential Salmonella Typhimurium Proteins, Ygjd & Yeaz And Calorimetric Evidence For The Formation Of A Ternary Ygjd-Yeaz-Yjee Complex.
Protein Sci. V. 22 628 2013
PubMed-ID: 23471679 | Reference-DOI: 10.1002/PRO.2247

Molecule 1 - PUTATIVE M22 PEPTIDASE YEAZ
	Chains	:	A, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
	Organism Taxid	:	909946
	Strain	:	STRAIN 4/74
	Synonym	:	YEAZ

Molecule 2 - PROBABLE TRNA THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN GCP
	Chains	:	B, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
	Organism Taxid	:	909946
	Other Details	:	TITLE STRUCTURE OF A SALMONELLA TYPHIMURIUM YGJD-YEAZ HETERODIMER BOUND TO ATPGAMMAS
	Synonym	:	T(6)A37 THREONYLCARBAMOYLADENOSINE BIOSYNTHESIS PROTEIN, YGJD

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 24)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	AGS	2	Ligand/Ion	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
3	CL	4	Ligand/Ion	CHLORIDE ION
4	MG	4	Ligand/Ion	MAGNESIUM ION
5	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
6	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 7)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	AGS	1	Ligand/Ion	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 7)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	AGS	1	Ligand/Ion	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
6	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:108 , THR A:109 , ARG A:110 , HOH A:2089 , HOH A:2129	BINDING SITE FOR RESIDUE CL A 1231
02	AC2	SOFTWARE	ARG B:326 , PRO B:327 , ARG B:328	BINDING SITE FOR RESIDUE CL B 1338
03	AC3	SOFTWARE	HIS B:111 , HIS B:115 , ASP B:300 , AGS B:1342	BINDING SITE FOR RESIDUE ZN B 1339
04	AC4	SOFTWARE	ASP B:11 , GLU B:12 , HOH B:2015 , HOH B:2016 , HOH B:2017 , HOH B:2020	BINDING SITE FOR RESIDUE MG B 1340
05	AC5	SOFTWARE	TRP A:224 , PRO B:44 , GLU B:45	BINDING SITE FOR RESIDUE CL B 1341
06	AC6	SOFTWARE	HIS B:111 , MET B:112 , HIS B:115 , SER B:136 , GLY B:137 , GLY B:138 , HIS B:139 , GLY B:163 , PHE B:166 , ASP B:167 , GLY B:180 , PRO B:181 , GLY B:268 , VAL B:269 , ASN B:272 , CYS B:298 , THR B:299 , ASP B:300 , ZN B:1339 , HOH B:2009 , HOH B:2011 , HOH B:2015 , HOH B:2020 , HOH B:2099 , HOH B:2168 , HOH B:2261 , HOH B:2262 , HOH B:2263 , HOH B:2264	BINDING SITE FOR RESIDUE AGS B 1342
07	AC7	SOFTWARE	TRP D:224 , PRO E:44 , GLU E:45	BINDING SITE FOR RESIDUE CL E 1338
08	AC8	SOFTWARE	HIS E:111 , HIS E:115 , ASP E:300 , AGS E:1341	BINDING SITE FOR RESIDUE ZN E 1339
09	AC9	SOFTWARE	ASP E:11 , GLU E:12 , HOH E:2014 , HOH E:2015 , HOH E:2016 , HOH E:2019	BINDING SITE FOR RESIDUE MG E 1340
10	BC1	SOFTWARE	HIS E:111 , MET E:112 , HIS E:115 , SER E:136 , GLY E:137 , GLY E:138 , HIS E:139 , GLY E:163 , PHE E:166 , ASP E:167 , GLY E:180 , PRO E:181 , GLY E:268 , VAL E:269 , ASN E:272 , THR E:299 , ASP E:300 , ZN E:1339 , HOH E:2006 , HOH E:2008 , HOH E:2014 , HOH E:2019 , HOH E:2098 , HOH E:2125 , HOH E:2162 , HOH E:2246 , HOH E:2247 , HOH E:2248	BINDING SITE FOR RESIDUE AGS E 1341
11	BC2	SOFTWARE	HOH B:2139 , HOH B:2140 , HOH B:2141 , HOH B:2142 , HOH B:2265	BINDING SITE FOR RESIDUE MG B 1380
12	BC3	SOFTWARE	HOH A:2170 , HOH E:2137 , HOH E:2138 , HOH E:2249	BINDING SITE FOR RESIDUE MG E 1380

(no "SS Bond" information available for 3ZEU)

Asymmetric Unit

No.	Residues
1	Gly A:64	-	Pro A:65
2	Gly B:81	-	Pro B:82
3	Phe B:128	-	Pro B:129
4	Tyr B:177	-	Pro B:178
5	Gly D:64	-	Pro D:65
6	Gly E:81	-	Pro E:82
7	Phe E:128	-	Pro E:129
8	Tyr E:177	-	Pro E:178

(no "SAP(SNP)/Variant" information available for 3ZEU)

(no "PROSITE Motif" information available for 3ZEU)

(no "Exon" information available for 3ZEU)

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:235
 aligned with E8X8J1_SALT4 | E8X8J1 from UniProtKB/TrEMBL  Length:231

    Alignment length:235
                                                                    41                                               89        98                   119                                                                         194                                    
                                                                  40 |                                             88 |      97 |                 118 |                                                                       193 |                                    
                                    10        20        30        40 |      49        59        69        79        |-|       |-|      107       117| |    126       136       146       156       166       176       186      |195       205       215       225     
         E8X8J1_SALT4     1 MRILAIDTATEACSVALWNNGTINAHFELCPREHTQRILP-MVQEILAASGASLNEIDALAFGRGPGSFTGVRIGIGIAQGLALGANLP-MIGVSTLAT-MAQGAWRKTGATRVLAAIDAR-MGEVYWAEYQRDAQGVWQGEETEAVLKPERVGERLKQLSGEWATVGTGWSAWPDLAKECGLTLHDGEVSLPAAED-MLPIASQKLAAGETVAVEHAEPVYLRNEVAWKKLPGK 230
               SCOP domains d3zeua1 A:1-107 automated matches                                                                             d3zeua2 A:188-230 automated matches                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeeeeeee..eeeeeeee...hhhhhh..hhhhhhhhhhh.hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhh..eeeeeeeee...eeeeeeeee.....eehhhhheeehhhhhhhhhh....eeeee.hhhhhh.........eeee......hhhhhhhhhhhhhhhh....hhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zeu A   1 MRILAIDTATEACSVALWNNGTINAHFELCPREHTQRILPmMVQEILAASGASLNEIDALAFGRGPGSFTGVRIGIGIAQGLALGANLPmMIGVSTLATmMAQGAWRKTGATRVLAAIDARmMGEVYWAEYQRDAQGVWQGEETEAVLKPERVGERLKQLSGEWATVGTGWSAWPDLAKECGLTLHDGEVSLPAAEDmMLPIASQKLAAGETVAVEHAEPVYLRNEVAWKKLPGK 230
                                    10        20        30        40|       49        59        69        79        89        98       107       117 |     126       136       146       156       166       176       186       195       205       215       225     
                                                                   41-MSE                                           89-MSE    98-MSE               119-MSE                                                                     194-MSE

Chain B from PDB  Type:PROTEIN  Length:337
 aligned with E8XBD7_SALT4 | E8XBD7 from UniProtKB/TrEMBL  Length:337

    Alignment length:337
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       
         E8XBD7_SALT4     1 MRVLGIETSCDETGIAIYDDKKGLLANQLYSQVKLHADYGGVVPELASRDHVRKTVPLIQAALKEAGLTASDIDAVAYTAGPGLVGALLVGATVGRSLAFAWNVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQYELLGESIDDAAGEAFDKTAKLLGLDYPGGPMLSKMASQGTAGRFVFPRPMTDRPGLDFSFSGLKTFAANTIRSNGGDEQTRADIARAFEDAVVDTLMIKCKRALESTGFKRLVMAGGVSANRTLRAKLAEMMQKRRGEVFYARPEFCTDNGAMIAYAGMVRFKAGVTADLGVTVRPRWPLAELPAA 337
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeeee...eeeeeeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh.......eeeeee....eeeeeeee..eeeeeee....hhhhhhhhhhhhh.....hhhhhhhhhh......................hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh..eeee.hhhhh...hhhhhhhhhhhhhh..............hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zeu B   1 MRVLGIETSCDETGIAIYDDKKGLLANQLYSQVKLHADYGGVVPELASRDHVRKTVPLIQAALKEAGLTASDIDAVAYTAGPGLVGALLVGATVGRSLAFAWNVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQYELLGESIDDAAGEAFDKTAKLLGLDYPGGPMLSKMASQGTAGRFVFPRPMTDRPGLDFSFSGLKTFAANTIRSNGGDEQTRADIARAFEDAVVDTLMIKCKRALESTGFKRLVMAGGVSANRTLRAKLAEMMQKRRGEVFYARPEFCTDNGAMIAYAGMVRFKAGVTADLGVTVRPRWPLAELPAA 337
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330

Chain D from PDB  Type:PROTEIN  Length:235
 aligned with E8X8J1_SALT4 | E8X8J1 from UniProtKB/TrEMBL  Length:231

    Alignment length:235
                                                                    41                                               89        98                   119                                                                         194                                    
                                                                  40 |                                             88 |      97 |                 118 |                                                                       193 |                                    
                                    10        20        30        40 |      49        59        69        79        |-|       |-|      107       117| |    126       136       146       156       166       176       186      |195       205       215       225     
         E8X8J1_SALT4     1 MRILAIDTATEACSVALWNNGTINAHFELCPREHTQRILP-MVQEILAASGASLNEIDALAFGRGPGSFTGVRIGIGIAQGLALGANLP-MIGVSTLAT-MAQGAWRKTGATRVLAAIDAR-MGEVYWAEYQRDAQGVWQGEETEAVLKPERVGERLKQLSGEWATVGTGWSAWPDLAKECGLTLHDGEVSLPAAED-MLPIASQKLAAGETVAVEHAEPVYLRNEVAWKKLPGK 230
               SCOP domains d3zeud1 D:1-107 automated matches                                                                             d3zeud2 D:188-230 automated matches                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeeeeeee..eeeeeeee...hhhhhh..hhhhhhhhhh..hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhh..eeeeeeeee...eeeeeeeee.....eehhhhheeehhhhhhhhhh....eeeeehhhhhhh.........eeee......hhhhhhhhhhhhhhhh....hhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zeu D   1 MRILAIDTATEACSVALWNNGTINAHFELCPREHTQRILPmMVQEILAASGASLNEIDALAFGRGPGSFTGVRIGIGIAQGLALGANLPmMIGVSTLATmMAQGAWRKTGATRVLAAIDARmMGEVYWAEYQRDAQGVWQGEETEAVLKPERVGERLKQLSGEWATVGTGWSAWPDLAKECGLTLHDGEVSLPAAEDmMLPIASQKLAAGETVAVEHAEPVYLRNEVAWKKLPGK 230
                                    10        20        30        40|       49        59        69        79        89        98       107       117 |     126       136       146       156       166       176       186       195       205       215       225     
                                                                   41-MSE                                           89-MSE    98-MSE               119-MSE                                                                     194-MSE

Chain E from PDB  Type:PROTEIN  Length:337
 aligned with E8XBD7_SALT4 | E8XBD7 from UniProtKB/TrEMBL  Length:337

    Alignment length:337
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       
         E8XBD7_SALT4     1 MRVLGIETSCDETGIAIYDDKKGLLANQLYSQVKLHADYGGVVPELASRDHVRKTVPLIQAALKEAGLTASDIDAVAYTAGPGLVGALLVGATVGRSLAFAWNVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQYELLGESIDDAAGEAFDKTAKLLGLDYPGGPMLSKMASQGTAGRFVFPRPMTDRPGLDFSFSGLKTFAANTIRSNGGDEQTRADIARAFEDAVVDTLMIKCKRALESTGFKRLVMAGGVSANRTLRAKLAEMMQKRRGEVFYARPEFCTDNGAMIAYAGMVRFKAGVTADLGVTVRPRWPLAELPAA 337
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeeee...eeeeeeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh.......eeeeee....eeeeeeee..eeeeeee....hhhhhhhhhhhhh.....hhhhhhhhhh......................hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh..eeee.hhhhh...hhhhhhhhhhhhhh..............hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zeu E   1 MRVLGIETSCDETGIAIYDDKKGLLANQLYSQVKLHADYGGVVPELASRDHVRKTVPLIQAALKEAGLTASDIDAVAYTAGPGLVGALLVGATVGRSLAFAWNVPAIPVHHMEGHLLAPMLEDNPPEFPFVALLVSGGHTQLISVTGIGQYELLGESIDDAAGEAFDKTAKLLGLDYPGGPMLSKMASQGTAGRFVFPRPMTDRPGLDFSFSGLKTFAANTIRSNGGDEQTRADIARAFEDAVVDTLMIKCKRALESTGFKRLVMAGGVSANRTLRAKLAEMMQKRRGEVFYARPEFCTDNGAMIAYAGMVRFKAGVTADLGVTVRPRWPLAELPAA 337
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330

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 enterica [TaxId: 909946] (2)

1a	d3zeua1	A:1-107
1b	d3zeua2	A:108-230
1c	d3zeud1	D:1-107
1d	d3zeud2	D:108-230

(no "CATH Domain" information available for 3ZEU)

(no "Pfam Domain" information available for 3ZEU)

Asymmetric Unit(hide GO term definitions)

Chain A,D (E8X8J1_SALT4 | E8X8J1)

biological process
	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).

Chain B,E (E8XBD7_SALT4 | E8XBD7)

molecular function
	GO:0061711	N(6)-L-threonylcarbamoyladenine synthase	Catalysis of the reaction: L-threonylcarbamoyladenylate + adenine(37) in tRNA = AMP + N(6)-L-threonylcarbamoyladenine(37) in tRNA.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain 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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
	GO:0016747	transferase activity, transferring acyl groups other than amino-acyl groups	Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		ADP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		AGS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
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		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:64 - Pro A:65	[ RasMol ]
		Gly B:81 - Pro B:82	[ RasMol ]
		Gly D:64 - Pro D:65	[ RasMol ]
		Gly E:81 - Pro E:82	[ RasMol ]
		Phe B:128 - Pro B:129	[ RasMol ]
		Phe E:128 - Pro E:129	[ RasMol ]
		Tyr B:177 - Pro B:178	[ RasMol ]
		Tyr E:177 - Pro E:178	[ RasMol ]

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

Jmol
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Molscript
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Access by PDB/NDB ID
	3zeu
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	E8XBD7_SALT4 \| E8XBD7
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
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Access by UniProt ID/Accession number
	E8X8J1_SALT4 \| E8X8J1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	E8XBD7_SALT4 \| E8XBD7
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	E8X8J1_SALT4 \| E8X8J1	:	3zet
	E8XBD7_SALT4 \| E8XBD7	:	3zet

3zet	STRUCTURE OF A SALMONELLA TYPHIMURIUM YGJD-YEAZ HETERODIMER.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 24)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 13)

Visualization

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Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File