4G37 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF CROSS-LINKED FIREFLY LUCIFERASE IN SECOND CATALYTIC CONFORMATION

Authors :   J. A. Sundlov, B. R. Branchini, A. M. Gulick

Date :   13 Jul 12 (Deposition) - 15 Aug 12 (Release) - 31 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Anl Superfamily, Ligase, Adenylating Enzymes, Luciferase, Domain Alternation, Trapped Conformation, Chemical Cross-Linker (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. Sundlov, D. M. Fontaine, T. L. Southworth, B. R. Branchini, A. M. Gulick
Crystal Structure Of Firefly Luciferase In A Second Catalytic Conformation Supports A Domain Alternation Mechanism.
Biochemistry V. 51 6493 2012
PubMed-ID: 22852753 | Reference-DOI: 10.1021/BI300934S

Molecule 1 - LUCIFERIN 4-MONOOXYGENASE
	Chains	:	A, B
	EC Number	:	1.13.12.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PGEX-6P-2
	Mutation	:	YES
	Organism Common	:	NORTH AMERICAN FIREFLY
	Organism Scientific	:	PHOTINUS PYRALIS
	Organism Taxid	:	7054
	Synonym	:	LUCIFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	SLU	2	Ligand/Ion	5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE
3	SO4	4	Ligand/Ion	SULFATE ION
4	XLX	2	Ligand/Ion	4,4'-(ETHYLENEDIIMINO)BIS[4-OXOBUTYRATE]

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	SLU	1	Ligand/Ion	5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE
3	SO4	2	Ligand/Ion	SULFATE ION
4	XLX	1	Ligand/Ion	4,4'-(ETHYLENEDIIMINO)BIS[4-OXOBUTYRATE]

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	SLU	1	Ligand/Ion	5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE
3	SO4	2	Ligand/Ion	SULFATE ION
4	XLX	1	Ligand/Ion	4,4'-(ETHYLENEDIIMINO)BIS[4-OXOBUTYRATE]

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:245 , PHE A:247 , THR A:251 , SER A:314 , GLY A:315 , GLY A:316 , ALA A:317 , PRO A:318 , GLN A:338 , GLY A:339 , GLY A:341 , LEU A:342 , THR A:343 , ALA A:348 , ASP A:422 , ARG A:437 , LYS A:439 , LYS A:443 , GLN A:448 , HOH A:735 , HOH A:772 , HOH A:773	BINDING SITE FOR RESIDUE SLU A 601
2	AC2	SOFTWARE	CYS A:108 , LYS A:445 , CYS A:447	BINDING SITE FOR RESIDUE XLX A 602
3	AC3	SOFTWARE	TYR A:70 , LYS A:148 , GLN A:162 , HIS A:171	BINDING SITE FOR RESIDUE SO4 A 603
4	AC4	SOFTWARE	LYS A:380 , ARG A:393	BINDING SITE FOR RESIDUE SO4 A 604
5	AC5	SOFTWARE	HIS B:245 , PHE B:247 , THR B:251 , GLY B:315 , GLY B:316 , ALA B:317 , PRO B:318 , GLN B:338 , GLY B:339 , TYR B:340 , GLY B:341 , LEU B:342 , THR B:343 , ALA B:348 , ASP B:422 , LYS B:439 , LEU B:441 , LYS B:443 , GLN B:448 , HOH B:757 , HOH B:791 , HOH B:808	BINDING SITE FOR RESIDUE SLU B 601
6	AC6	SOFTWARE	CYS B:108 , LYS B:445 , CYS B:447	BINDING SITE FOR RESIDUE XLX B 602
7	AC7	SOFTWARE	ARG B:261 , HOH B:761	BINDING SITE FOR RESIDUE CL B 603
8	AC8	SOFTWARE	TYR B:70 , LYS B:148 , GLN B:162 , HIS B:171	BINDING SITE FOR RESIDUE SO4 B 604
9	AC9	SOFTWARE	ARG B:393 , ASP B:415 , TRP B:417	BINDING SITE FOR RESIDUE SO4 B 605

(no "SS Bond" information available for 4G37)

(no "Cis Peptide Bond" information available for 4G37)

(no "SAP(SNP)/Variant" information available for 4G37)

(no "PROSITE Motif" information available for 4G37)

(no "Exon" information available for 4G37)

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:533
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4g37a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...........hhhhhhhhhhhhhh.....eeeee....eeeehhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhh.eeeee....hhhhhhhhhhhhh..eeee...hhhhhhhhhhhh....eeee...........hhhhhhhhhh....hhhhh..........eeeeeee..eeeeeehhhhhhhhhhhh............eeee.....hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh...eeee..hhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh.....eeeee.hhhh.eeee............ee....eeeee.............eeeeee......ee..hhhhhhhhh.....eeeeeeeee.....eeeeee....eee..eeehhhhhhhhhhhh..eeeeeeeeeee...eeeeeeeeee......hhhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g37 A   4 AKNIKKGPAPFYPLEDGTAGEQLHKAMKRYALVPGTIAFTDAHIEVNITYAEYFEMSVRLAEAMKRYGLNTNHRIVVSSENSLQFFMPVLGALFIGVAVAPANDCYNERELLNSMNISQPTVVFVSKKGLQKILNVQKKLPIIQKIIIMDSKTDYQGFQSMYTFVTSHLPPGFNEYDFVPESFDRDKTIALIMNSSPKGVALPHRALAVRFSHARDPIFGNQIAPDTAILSVVPFHHGFGMFTTLGYLISGFRVVLMYRFEEELFLRSLQDYKIQSALLVPTLFSFLAKSTLIDKYDLSNLHEIASGGAPLSKEVGEAVAKRFHLPGIRQGYGLTETTSAILITPKGDDKPGAVGKVVPFFEAKVVDLDTGKTLGVNQRGELSVRGPMIMSGYVNNPEATNALIDKDGWLHSGDIAYWDEDEHFFIVDRLKSLIKYKGCQVAPAELESILLQHPNIFDAGVAGLPDDDAGELPAAVVVLEHGKTMTEKEIVDYVASQVTTAKKLRGGVVFVDEVPKGLKLDARKIREILIKAK 543
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193     ||208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       530       540   
                                                                                                                                                                                                                             199|                                                                                                                                                                                                                                                                                                                              526|              
                                                                                                                                                                                                                              205                                                                                                                                                                                                                                                                                                                               529

Chain B from PDB  Type:PROTEIN  Length:539
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4g37b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhee...........hhhhhhhhhhhhhhhh...eeeee....eeeehhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhh.eeeee....hhhhhhhhhhhhh..eeee...hhhhhhhhhh......eeee...........hhhhhhhh......hhhhh..........eeeeeee...eeeeeehhhhhhhhhhhhh...........eeee.....hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh...eeee.hhhhhhhhh..hhhhh......eeeee....hhhhhhhhhhhh.....eeeee.hhhh.eeee............ee....eeeee.............eeeeee......ee..hhhhhhhhh.....eeeeeeeee.....eeeeee....eee..eeehhhhhhhhhhhh..eeeeeeeeeee...eeeeeeeeee......hhhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g37 B   1 MEDAKNIKKGPAPFYPLEDGTAGEQLHKAMKRYALVPGTIAFTDAHIEVNITYAEYFEMSVRLAEAMKRYGLNTNHRIVVSSENSLQFFMPVLGALFIGVAVAPANDCYNERELLNSMNISQPTVVFVSKKGLQKILNVQKKLPIIQKIIIMDSKTDYQGFQSMYTFVTSHLPPGFNEYDFVPESFDRDKTIALIMNSSLPKGVALPHRALAVRFSHARDPIFGNQIAPDTAILSVVPFHHGFGMFTTLGYLISGFRVVLMYRFEEELFLRSLQDYKIQSALLVPTLFSFLAKSTLIDKYDLSNLHEIASGGAPLSKEVGEAVAKRFHLPGIRQGYGLTETTSAILITPKGDDKPGAVGKVVPFFEAKVVDLDTGKTLGVNQRGELSVRGPMIMSGYVNNPEATNALIDKDGWLHSGDIAYWDEDEHFFIVDRLKSLIKYKGCQVAPAELESILLQHPNIFDAGVAGLPDDDAGELPAAVVVLEHGKTMTEKEIVDYVASQVTTAKKLRGGVVFVDEVPKGLTGKLDARKIREILIKAK 543
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534         
                                                                                                                                                                                                                                199|                                                                                                                                                                                                                                                                                                                                                   
                                                                                                                                                                                                                                 204

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: Acetyl-CoA synthetase-like (64)

Superfamily: Acetyl-CoA synthetase-like (64)

Family: Acetyl-CoA synthetase-like (38)

Protein domain: automated matches (3)

Firefly (Photinus pyralis) [TaxId: 7054] (3)

1a	d4g37a_	A:
1b	d4g37b_	B:

(no "CATH Domain" information available for 4G37)

(no "Pfam Domain" information available for 4G37)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4g37)

Biological Units
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	4g37
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	1.13.12.7
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	LUCI_PHOPY \| P08659	:	1ba3 1lci 3iep 3ier 3ies 3rix 4e5d 4g36 5dv9 5dwv 5kyt 5kyv

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

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Gene Ontology (11, 11)

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