4J4H - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   PYLD IN COMPLEX WITH PYRROLINE-CARBOXY-LYSINE AND NADH

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

Date :   06 Feb 13 (Deposition) - 12 Jun 13 (Release) - 10 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: A (1x),B (1x),C (1x),D (1x)

Keywords :   Pyrrolysine, 22Nd Amino Acid, Biosynthesis, Rossmann Fold, Dehydrogenase, Nadh, Pyrroline-Carboxy-Lysine, 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, C, D
	EC Number	:	1.4.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET28B
	Gene	:	MBAR_A0835
	Organism Scientific	:	METHANOSARCINA BARKERI
	Organism Taxid	:	269797
	Strain	:	FUSARO

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 16)

No.	Name	Count	Type	Full Name
1	1J1	4	Ligand/Ion	N~6~-[(2R)-3,4-DIHYDRO-2H-PYRROL-2-YLCARBONYL]-L-LYSINE
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	NA	4	Ligand/Ion	SODIUM ION
4	NAI	4	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	1J1	1	Ligand/Ion	N~6~-[(2R)-3,4-DIHYDRO-2H-PYRROL-2-YLCARBONYL]-L-LYSINE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	NAI	1	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	1J1	1	Ligand/Ion	N~6~-[(2R)-3,4-DIHYDRO-2H-PYRROL-2-YLCARBONYL]-L-LYSINE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	NAI	1	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	1J1	1	Ligand/Ion	N~6~-[(2R)-3,4-DIHYDRO-2H-PYRROL-2-YLCARBONYL]-L-LYSINE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	NAI	1	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	1J1	1	Ligand/Ion	N~6~-[(2R)-3,4-DIHYDRO-2H-PYRROL-2-YLCARBONYL]-L-LYSINE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	NAI	1	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	1J1	-1	Ligand/Ion	N~6~-[(2R)-3,4-DIHYDRO-2H-PYRROL-2-YLCARBONYL]-L-LYSINE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	NA	-1	Ligand/Ion	SODIUM ION
4	NAI	-1	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:2 , ASN A:121 , VAL A:147 , GLY A:150 , LYS A:151 , VAL A:152 , TYR A:170 , ASP A:171 , ALA A:172 , ASP A:173 , 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 , 1J1 A:902 , MG A:904 , HOH A:1001 , HOH A:1002 , HOH A:1005 , HOH A:1091 , HOH A:1113 , HOH A:1166 , HOH A:1186 , HOH C:1041 , HOH C:1058	BINDING SITE FOR RESIDUE NAI A 901
02	AC2	SOFTWARE	LEU A:3 , LEU A:4 , PRO A:52 , VAL A:53 , GLY A:58 , ILE A:59 , ILE A:60 , PHE A:63 , ALA A:103 , NAI A:901 , HOH A:1011 , HOH A:1013 , HOH A:1040 , HOH A:1042 , HOH A:1051 , HOH A:1166	BINDING SITE FOR RESIDUE 1J1 A 902
03	AC3	SOFTWARE	GLU A:202 , THR A:204 , CYS A:206 , PRO A:227	BINDING SITE FOR RESIDUE NA A 903
04	AC4	SOFTWARE	TYR A:129 , GLU A:245 , LEU A:247 , ILE A:249 , GLY A:250 , NAI A:901	BINDING SITE FOR RESIDUE MG A 904
05	AC5	SOFTWARE	ALA B:2 , 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 , THR B:209 , PRO B:224 , ILE B:226 , GLU B:245 , PRO B:246 , LEU B:247 , 1J1 B:902 , MG B:904 , HOH B:1001 , HOH B:1003 , HOH B:1036 , HOH B:1042 , HOH B:1082 , HOH B:1105 , HOH B:1125 , HOH B:1128 , HOH B:1142 , HOH B:1155 , HOH B:1163 , HOH B:1165	BINDING SITE FOR RESIDUE NAI B 901
06	AC6	SOFTWARE	LEU B:3 , LEU B:4 , VAL B:53 , GLY B:58 , ILE B:59 , ILE B:60 , PHE B:63 , ALA B:103 , NAI B:901 , HOH B:1006 , HOH B:1017 , HOH B:1022 , HOH B:1077 , HOH B:1081	BINDING SITE FOR RESIDUE 1J1 B 902
07	AC7	SOFTWARE	GLU B:202 , THR B:204 , CYS B:206 , PRO B:227	BINDING SITE FOR RESIDUE NA B 903
08	AC8	SOFTWARE	TYR B:129 , GLU B:245 , LEU B:247 , ILE B:249 , GLY B:250 , NAI B:901	BINDING SITE FOR RESIDUE MG B 904
09	AC9	SOFTWARE	MET C:1 , ALA C:2 , ASN C:121 , VAL C:147 , GLY C:148 , GLY C:150 , LYS C:151 , VAL C:152 , TYR C:170 , ASP C:171 , ALA C:172 , ASP C:173 , LEU C:176 , ALA C:203 , THR C:204 , PRO C:205 , CYS C:206 , THR C:209 , PRO C:224 , ILE C:226 , GLU C:245 , PRO C:246 , 1J1 C:902 , MG C:904 , HOH C:1001 , HOH C:1002 , HOH C:1006 , HOH C:1017 , HOH C:1022 , HOH C:1024	BINDING SITE FOR RESIDUE NAI C 901
10	BC1	SOFTWARE	LEU C:3 , LEU C:4 , PRO C:52 , VAL C:53 , GLY C:58 , ILE C:59 , ILE C:60 , PHE C:63 , ALA C:103 , NAI C:901 , HOH C:1004 , HOH C:1013 , HOH C:1015 , HOH C:1016 , HOH C:1021	BINDING SITE FOR RESIDUE 1J1 C 902
11	BC2	SOFTWARE	GLU C:202 , THR C:204 , CYS C:206 , PRO C:227	BINDING SITE FOR RESIDUE NA C 903
12	BC3	SOFTWARE	TYR C:129 , GLU C:245 , LEU C:247 , ILE C:249 , GLY C:250 , NAI C:901	BINDING SITE FOR RESIDUE MG C 904
13	BC4	SOFTWARE	HOH B:1124 , HOH B:1130 , MET D:1 , ALA D:2 , ASN D:121 , VAL D:147 , GLY D:150 , LYS D:151 , VAL D:152 , TYR D:170 , ASP D:171 , ALA D:172 , ALA D:203 , THR D:204 , PRO D:205 , CYS D:206 , THR D:209 , PRO D:224 , ILE D:226 , GLU D:245 , PRO D:246 , 1J1 D:902 , MG D:904 , HOH D:1001 , HOH D:1005 , HOH D:1009 , HOH D:1024 , HOH D:1025 , HOH D:1040	BINDING SITE FOR RESIDUE NAI D 901
14	BC5	SOFTWARE	LEU D:4 , PRO D:52 , VAL D:53 , GLY D:58 , ILE D:59 , ILE D:60 , PHE D:63 , ALA D:103 , ASP D:104 , NAI D:901 , HOH D:1002 , HOH D:1003 , HOH D:1006 , HOH D:1014 , HOH D:1036	BINDING SITE FOR RESIDUE 1J1 D 902
15	BC6	SOFTWARE	GLU D:202 , THR D:204 , CYS D:206 , PRO D:227	BINDING SITE FOR RESIDUE NA D 903
16	BC7	SOFTWARE	TYR D:129 , GLU D:245 , LEU D:247 , ILE D:249 , GLY D:250 , NAI D:901	BINDING SITE FOR RESIDUE MG D 904

(no "SS Bond" information available for 4J4H)

Asymmetric Unit

No.	Residues
1	Ile A:226	-	Pro A:227
2	Ile B:226	-	Pro B:227
3	Ile C:226	-	Pro C:227
4	Ile D:226	-	Pro D:227

(no "SAP(SNP)/Variant" information available for 4J4H)

(no "PROSITE Motif" information available for 4J4H)

(no "Exon" information available for 4J4H)

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:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......eeee...........hhhhhhhhhhhhh..eeee...hhhhhhhhhhhh...eeeee....eeeee.....eeehhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh.ee........eeeeee........hhh.eeeeeeee........hhhhhhhh..eee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j4h A   1 MALLTPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGIVPVTSGNGIIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEIILMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGLGKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSIIFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIGTASMLYSVL 259
                                    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

Chain B from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......eeee...........hhhhhhhhhhhhh..eeee...hhhhhhhhhhhh...eeeee....eeeee.....eeehhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh.ee........eeeeee........hhh.eeeeeeee........hhhhhhhh..eee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j4h B   1 MALLTPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGIVPVTSGNGIIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEIILMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGLGKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSIIFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIGTASMLYSVL 259
                                    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

Chain C from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......eeeee..........hhhhhhhhhhhhh..eeee...hhhhhhhhhhhh...eeeee....eeeee.....eeehhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh.ee........eeeeee........hhh.eeeeeeee........hhhhhhhh..eee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j4h C   1 MALLTPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGIVPVTSGNGIIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEIILMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGLGKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSIIFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIGTASMLYSVL 259
                                    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

Chain D from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......eeee...........hhhhhhhhhhhhh..eeee...hhhhhhhhhhhh...eeeee....eeeee.....eeehhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhh...eeeee..hhhhhhhhhhhh..ee........eeeeee........hhh.eeeeeeee........hhhhhhhh..eee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j4h D   1 MALLTPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGIVPVTSGNGIIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEIILMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGLGKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSIIFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIGTASMLYSVL 259
                                    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

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4J4H)

(no "CATH Domain" information available for 4J4H)

(no "Pfam Domain" information available for 4J4H)

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Asymmetric Unit
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	Cis Peptide Bonds
		Ile A:226 - Pro A:227	[ RasMol ]
		Ile B:226 - Pro B:227	[ RasMol ]
		Ile C:226 - Pro C:227	[ RasMol ]
		Ile D:226 - Pro D:227	[ RasMol ]

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	Q46E80_METBF \| Q46E80	:	4j43 4j49 4j4b 4jk3 4q39 4q3a 4q3b 4q3c 4q3d 4q3e

3t7v	PYLB IN COMPLEX WITH 3R-METHYL-D-ORNITHINE
4ffp	PYLC IN COMPLEX WITH L-LYSINE-NE-D-ORNITHINE
4j43
4j49
4j4b

Description

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Ligands, Modified Residues, Ions (4, 16)

Sites (16, 16)

SS Bonds (0, 0)

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