4JK3 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   PYLD HOLOENZYME (SEMET)

Authors :   F. Quitterer, P. Beck, A. Bacher, M. Groll

Date :   09 Mar 13 (Deposition) - 12 Jun 13 (Release) - 10 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Pyrrolysine, 22Nd Amino Acid, Biosynthesis, Rossmann Fold, Dehydrogenase, Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Quitterer, P. Beck, A. Bacher, M. Groll
Structure And Reaction Mechanism Of Pyrrolysine Synthase (Pyld).
Angew. Chem. Int. Ed. Engl. V. 52 7033 2013
PubMed-ID: 23720358 | Reference-DOI: 10.1002/ANIE.201301164

Molecule 1 - PYLD
	Chains	:	A, B
	EC Number	:	1.4.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	MBAR_A0835
	Organism Scientific	:	METHANOSARCINA BARKERI
	Organism Taxid	:	269797
	Strain	:	FUSARO

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 16)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
3	NA	2	Ligand/Ion	SODIUM ION
4	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION
4	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION
4	NAD	1	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 3 (2, 24)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION
4	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:121 , THR A:125 , VAL A:147 , GLY A:150 , LYS A:151 , VAL A:152 , ASP A:171 , ALA A:172 , LEU A:176 , ALA A:203 , THR A:204 , PRO A:205 , CYS A:206 , THR A:209 , PRO A:224 , ILE A:226 , GLU A:245 , PRO A:246 , LEU A:247 , MG A:903 , HOH A:1002 , HOH A:1011 , HOH A:1025	BINDING SITE FOR RESIDUE NAD A 901
2	AC2	SOFTWARE	GLU A:202 , THR A:204 , CYS A:206 , GLY A:225 , PRO A:227 , HOH A:1019	BINDING SITE FOR RESIDUE NA A 902
3	AC3	SOFTWARE	TYR A:129 , GLU A:245 , LEU A:247 , ILE A:249 , GLY A:250 , NAD A:901	BINDING SITE FOR RESIDUE MG A 903
4	AC4	SOFTWARE	ASN B:121 , THR B:125 , VAL B:147 , GLY B:150 , LYS B:151 , VAL B:152 , TYR B:170 , ASP B:171 , ALA B:172 , LEU B:176 , ALA B:203 , THR B:204 , PRO B:205 , CYS B:206 , PRO B:224 , ILE B:226 , GLU B:245 , PRO B:246 , LEU B:247 , MG B:903 , HOH B:1001	BINDING SITE FOR RESIDUE NAD B 901
5	AC5	SOFTWARE	GLU B:202 , THR B:204 , CYS B:206 , PRO B:227 , HOH B:1019	BINDING SITE FOR RESIDUE NA B 902
6	AC6	SOFTWARE	TYR B:129 , GLU B:245 , LEU B:247 , ILE B:249 , GLY B:250 , NAD B:901	BINDING SITE FOR RESIDUE MG B 903

(no "SS Bond" information available for 4JK3)

Asymmetric Unit

No.	Residues
1	Ile A:226	-	Pro A:227
2	Ile B:226	-	Pro B:227

(no "SAP(SNP)/Variant" information available for 4JK3)

(no "PROSITE Motif" information available for 4JK3)

(no "Exon" information available for 4JK3)

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:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......eeee......hhhhhhhhhhhhhh..eeee...hhhhhhhhhhhh...eeeee....eeeee.....eeehhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh.ee........eeeeee........hhh.eeeeeeee........hhhhhhhh..eee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jk3 A   5 TPDDLININmQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGIVPVTSIGNFSASLHAITQYFGFDSFVTDmPDVSGYYEAVQNGAEIILmADDRTFLAHNLKNGKmANNQPCTGIIYAEIASRYLKADSKDVLVVGLGKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSIIFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIGTASmLYSVL 259
                                    14        24        34        44        54||      68        78    |   88        98   |   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248     | 258 
                                    14-MSE                                   55|                     83-MSE            102-MSE         118-MSE                                                                                                                                 254-MSE 
                                                                              60

Chain B from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......eeee......hhhhhhhhhhhhhh..eeee...hhhhhhhhhhhh...eeeee....eeeee.....eeehhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh.ee........eeeeee........hhh.eeeeeeee........hhhhhhhhh.eee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jk3 B   5 TPDDLININmQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGIVPVTSIGNFSASLHAITQYFGFDSFVTDmPDVSGYYEAVQNGAEIILmADDRTFLAHNLKNGKmANNQPCTGIIYAEIASRYLKADSKDVLVVGLGKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSIIFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIGTASmLYSVL 259
                                    14        24        34        44        54||      68        78    |   88        98   |   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248     | 258 
                                    14-MSE                                   55|                     83-MSE            102-MSE         118-MSE                                                                                                                                 254-MSE 
                                                                              60

Legend:		→ Mismatch	(orange background)
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	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 '\|'

(no "SCOP Domain" information available for 4JK3)

(no "CATH Domain" information available for 4JK3)

(no "Pfam Domain" information available for 4JK3)

Asymmetric Unit(hide GO term definitions)

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	Cis Peptide Bonds
		Ile A:226 - Pro A:227	[ RasMol ]
		Ile B:226 - Pro B:227	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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	Q46E80_METBF \| Q46E80	:	4j43 4j49 4j4b 4j4h 4q39 4q3a 4q3b 4q3c 4q3d 4q3e

4j43	PYLD HOLOENZYME (NATIVE DATASET, 2.2 A RESOLUTION)
4j49
4j4b
4j4h

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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