4QS5 - JenaLib

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Title :   CRYSTAL STRUCTURE OF 5-CARBOXYVANILLATE DECARBOXYLASE LIGW2 FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 (TARGET EFI-505250) WITH BOUND MANGANESE AND 3-METHOXY-4-HYDROXY-5-NITROBENZOIC ACID, THE D314N MUTANT

Authors :   Y. Patskovsky, A. Vladimirova, R. Toro, R. Bhosle, B. Hillerich, R. D. S M. Raushel, S. C. Almo

Date :   02 Jul 14 (Deposition) - 06 Aug 14 (Release) - 06 Aug 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Amidohydrolase, Metal Binding Site, Decarboxylase, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Patskovsky, A. Vladimirova, R. Toro, R. Bhosle, J. A. Gerlt, F. M. Raushel, S. C. Almo
Crystal Structure Of 5-Carboxyvanillate Decarboxylase From Novosphingobium Aromaticivorans
To Be Published
PubMed: search

Molecule 1 - LIGW2 DECARBOXYLASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PLASMID
	Expression System Vector Type	:	PET
	Gene	:	SARO_0799
	Organism Scientific	:	NOVOSPHINGOBIUM AROMATICIVORANS
	Organism Taxid	:	279238
	Strain	:	DSM 12444 / F199

		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 (5, 20)

No.	Name	Count	Type	Full Name
1	1DF	4	Ligand/Ion	4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID
2	ACT	2	Ligand/Ion	ACETATE ION
3	CL	2	Ligand/Ion	CHLORIDE ION
4	GOL	8	Ligand/Ion	GLYCEROL
5	MN	4	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	1DF	2	Ligand/Ion	4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID
2	ACT	1	Ligand/Ion	ACETATE ION
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	GOL	3	Ligand/Ion	GLYCEROL
5	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (3, 8)

No.	Name	Count	Type	Full Name
1	1DF	2	Ligand/Ion	4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID
2	ACT	1	Ligand/Ion	ACETATE ION
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	GOL	5	Ligand/Ion	GLYCEROL
5	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:19 , HIS A:188 , ASN A:314 , 1DF A:402 , HOH A:695	BINDING SITE FOR RESIDUE MN A 401
02	AC2	SOFTWARE	GLU A:19 , TYR A:51 , ARG A:58 , THR A:90 , SER A:91 , HIS A:188 , HIS A:241 , ASN A:314 , TYR A:317 , MN A:401 , HOH A:513 , HOH A:593 , ARG B:252 , MET B:256 , HOH B:754	BINDING SITE FOR RESIDUE 1DF A 402
03	AC3	SOFTWARE	ASP A:41 , GLN A:162 , PRO A:193 , ASP A:194 , HOH A:590	BINDING SITE FOR RESIDUE GOL A 403
04	AC4	SOFTWARE	TYR A:121 , PRO A:122 , ASP A:123	BINDING SITE FOR RESIDUE CL A 404
05	AC5	SOFTWARE	HIS A:257 , GLN A:258 , PRO A:271 , LEU A:272 , HOH A:572 , HOH A:607	BINDING SITE FOR RESIDUE ACT A 405
06	AC6	SOFTWARE	GLU B:19 , HIS B:188 , ASN B:314 , 1DF B:402 , HOH B:708	BINDING SITE FOR RESIDUE MN B 401
07	AC7	SOFTWARE	ARG A:252 , MET A:256 , GLU B:19 , LEU B:47 , TYR B:51 , THR B:90 , SER B:91 , HIS B:188 , ALA B:208 , HIS B:241 , ASN B:314 , TYR B:317 , MN B:401 , HOH B:509 , HOH B:571 , HOH B:620 , HOH B:709	BINDING SITE FOR RESIDUE 1DF B 402
08	AC8	SOFTWARE	ASP B:307 , LYS B:339 , THR B:343 , ASN B:344 , LYS B:347	BINDING SITE FOR RESIDUE GOL B 403
09	AC9	SOFTWARE	ASP B:41 , GLN B:162 , PRO B:193 , ASP B:194 , HOH B:634	BINDING SITE FOR RESIDUE GOL B 404
10	BC1	SOFTWARE	TYR B:121 , ASP B:123	BINDING SITE FOR RESIDUE CL B 405
11	BC2	SOFTWARE	GLU C:19 , HIS C:188 , ASN C:314 , 1DF C:402 , HOH C:726	BINDING SITE FOR RESIDUE MN C 401
12	BC3	SOFTWARE	GLU C:19 , TYR C:51 , THR C:90 , SER C:91 , HIS C:188 , ALA C:208 , HIS C:241 , ASN C:314 , TYR C:317 , MN C:401 , HOH C:524 , HOH C:579 , ARG D:252 , MET D:256	BINDING SITE FOR RESIDUE 1DF C 402
13	BC4	SOFTWARE	ASP C:41 , GLN C:162 , PRO C:193 , ASP C:194 , HOH C:663	BINDING SITE FOR RESIDUE GOL C 403
14	BC5	SOFTWARE	ASP C:307 , LYS C:339 , THR C:343 , ASN C:344 , LYS C:347	BINDING SITE FOR RESIDUE GOL C 404
15	BC6	SOFTWARE	HIS C:257 , PRO C:271 , LEU C:272 , HOH C:666 , HOH C:679	BINDING SITE FOR RESIDUE ACT C 405
16	BC7	SOFTWARE	GLU D:19 , HIS D:188 , ASN D:314 , 1DF D:402 , HOH D:710	BINDING SITE FOR RESIDUE MN D 401
17	BC8	SOFTWARE	ARG C:252 , MET C:256 , HOH C:761 , GLU D:19 , TYR D:51 , THR D:90 , SER D:91 , HIS D:188 , PHE D:212 , HIS D:241 , ASN D:314 , TYR D:317 , MN D:401 , HOH D:527 , HOH D:711	BINDING SITE FOR RESIDUE 1DF D 402
18	BC9	SOFTWARE	ASP D:41 , GLN D:162 , PRO D:193 , ASP D:194 , HOH D:699	BINDING SITE FOR RESIDUE GOL D 403
19	CC1	SOFTWARE	GLU C:277 , TRP D:293 , HOH D:748	BINDING SITE FOR RESIDUE GOL D 404
20	CC2	SOFTWARE	ASP D:307 , LYS D:339 , THR D:343 , ASN D:344	BINDING SITE FOR RESIDUE GOL D 405

(no "SS Bond" information available for 4QS5)

Asymmetric Unit

No.	Residues
1	Ser A:91	-	Pro A:92
2	Tyr A:315	-	Pro A:316
3	Ser B:91	-	Pro B:92
4	Tyr B:315	-	Pro B:316
5	Ser C:91	-	Pro C:92
6	Tyr C:315	-	Pro C:316
7	Ser D:91	-	Pro D:92
8	Tyr D:315	-	Pro D:316

(no "SAP(SNP)/Variant" information available for 4QS5)

(no "PROSITE Motif" information available for 4QS5)

(no "Exon" information available for 4QS5)

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:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhh.....eee..........hhhhhhhhhhhhhhh..eee.........hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhheeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qs5 A   3 QDLKTGGEQGYLRIATEEAFATREIIDVYLRMIRDGTADKGMVSLWGFYAQSPSERATQILERLLDLGERRIADMDATGIDKAILALTSPGVQPLHDLDEARTLATRANDTLADACQKYPDRFIGMGTVAPQDPEWSAREIHRGARELGFKGIQINSHTQGRYLDEEFFDPIFRALVEVDQPLYIHPATSPDSMIDPMLEAGLDGAIFGFGVETGMHLLRLITIGIFDKYPSLQIMVGHMGEALPYWLYRLDYMHQAGVRSQRYERMKPLKKTIEGYLKSNVLVTNSGVAWEPAIKFCQQVMGEDRVMYAMNYPYQYVADEVRAMDAMDMSAQTKKKFFQTNAEKWFKL 351
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342

Chain B from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhh....eeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhh.....eee..........hhhhhhhhhhhhhhh..eee.........hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhheeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qs5 B   3 QDLKTGGEQGYLRIATEEAFATREIIDVYLRMIRDGTADKGMVSLWGFYAQSPSERATQILERLLDLGERRIADMDATGIDKAILALTSPGVQPLHDLDEARTLATRANDTLADACQKYPDRFIGMGTVAPQDPEWSAREIHRGARELGFKGIQINSHTQGRYLDEEFFDPIFRALVEVDQPLYIHPATSPDSMIDPMLEAGLDGAIFGFGVETGMHLLRLITIGIFDKYPSLQIMVGHMGEALPYWLYRLDYMHQAGVRSQRYERMKPLKKTIEGYLKSNVLVTNSGVAWEPAIKFCQQVMGEDRVMYAMNYPYQYVADEVRAMDAMDMSAQTKKKFFQTNAEKWFKL 351
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342

Chain C from PDB  Type:PROTEIN  Length:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhh..eee.....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhheeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qs5 C   4 DLKTGGEQGYLRIATEEAFATREIIDVYLRMIRDGTADKGMVSLWGFYAQSPSERATQILERLLDLGERRIADMDATGIDKAILALTSPGVQPLHDLDEARTLATRANDTLADACQKYPDRFIGMGTVAPQDPEWSAREIHRGARELGFKGIQINSHTQGRYLDEEFFDPIFRALVEVDQPLYIHPATSPDSMIDPMLEAGLDGAIFGFGVETGMHLLRLITIGIFDKYPSLQIMVGHMGEALPYWLYRLDYMHQAGVRSQRYERMKPLKKTIEGYLKSNVLVTNSGVAWEPAIKFCQQVMGEDRVMYAMNYPYQYVADEVRAMDAMDMSAQTKKKFFQTNAEKWFKL 351
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343

Chain D from PDB  Type:PROTEIN  Length:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhh.....eee..........hhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhheeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qs5 D   4 DLKTGGEQGYLRIATEEAFATREIIDVYLRMIRDGTADKGMVSLWGFYAQSPSERATQILERLLDLGERRIADMDATGIDKAILALTSPGVQPLHDLDEARTLATRANDTLADACQKYPDRFIGMGTVAPQDPEWSAREIHRGARELGFKGIQINSHTQGRYLDEEFFDPIFRALVEVDQPLYIHPATSPDSMIDPMLEAGLDGAIFGFGVETGMHLLRLITIGIFDKYPSLQIMVGHMGEALPYWLYRLDYMHQAGVRSQRYERMKPLKKTIEGYLKSNVLVTNSGVAWEPAIKFCQQVMGEDRVMYAMNYPYQYVADEVRAMDAMDMSAQTKKKFFQTNAEKWFKL 351
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343

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 4QS5)

(no "CATH Domain" information available for 4QS5)

(no "Pfam Domain" information available for 4QS5)

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	Cis Peptide Bonds
		Ser A:91 - Pro A:92	[ RasMol ]
		Ser B:91 - Pro B:92	[ RasMol ]
		Ser C:91 - Pro C:92	[ RasMol ]
		Ser D:91 - Pro D:92	[ RasMol ]
		Tyr A:315 - Pro A:316	[ RasMol ]
		Tyr B:315 - Pro B:316	[ RasMol ]
		Tyr C:315 - Pro C:316	[ RasMol ]
		Tyr D:315 - Pro D:316	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (5, 20)

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SS Bonds (0, 0)

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