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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL AND SOLUTION STRUCTURES OF THE BIFUNCTIONAL ENZYME (ALDOLASE/ALDEHYDE DEHYDROGENASE) FROM THERMOMONOSPORA CURVATA, REVEAL A COFACTOR-BINDING DOMAIN MOTION DURING NAD+ AND COA ACCOMMODATION WHITHIN THE SHARED COFACTOR-BINDING SITE

Authors :   B. Fischer, G. Branlant, F. Talfournier, A. Gruez

Date :   20 Jul 13 (Deposition) - 04 Sep 13 (Release) - 04 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Rosmmann Fold, Tim Barrel, Dehydrogenase, Aldolase, Lyase- Oxidoreductase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Fischer, G. Branlant, F. Talfournier, A. Gruez
Crystal And Solution Structures Of The Bifunctional Enzyme (Aldolase/Aldehyde Dehydrogenase) From Thermomonospora Curvata, Reveal A Cofactor-Binding Domain Motion During Nad And Coa Accommodation Whithin The Shared Cofactor-Binding Site
To Be Published
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Molecule 1 - 4-HYDROXY-2-OXOVALERATE ALDOLASE
	Chains	:	A, C
	EC Number	:	4.1.3.39
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	C41 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TCUR_0536
	Organism Scientific	:	THERMOMONOSPORA CURVATA
	Organism Taxid	:	471852
	Strain	:	DSM 43183
	Synonym	:	HOA, 4-HYDROXY-2-KETO-PENTANOIC ACID ALDOLASE, 4-HYDROXY-2- OXOPENTANOATE ALDOLASE

Molecule 2 - ACETALDEHYDE DEHYDROGENASE
	Chains	:	B, D
	EC Number	:	1.2.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	C41 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TCUR_0535
	Organism Scientific	:	THERMOMONOSPORA CURVATA
	Organism Taxid	:	471852
	Strain	:	DSM 43183
	Synonym	:	ACETALDEHYDE DEHYDROGENASE [ACETYLATING]

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 15)

No.	Name	Count	Type	Full Name
1	COA	2	Ligand/Ion	COENZYME A
2	GOL	3	Ligand/Ion	GLYCEROL
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	NA	4	Ligand/Ion	SODIUM ION
5	PYR	2	Ligand/Ion	PYRUVIC ACID
6	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:21 , ASP A:22 , MET A:145 , VAL A:173 , SER A:175 , HIS A:204 , HIS A:206 , TYR A:295 , MG A:403 , HOH A:543	BINDING SITE FOR RESIDUE PYR A 401
02	AC2	SOFTWARE	VAL A:180 , SER A:182 , GLN C:221 , HOH C:622	BINDING SITE FOR RESIDUE NA A 402
03	AC3	SOFTWARE	ASP A:22 , HIS A:204 , HIS A:206 , PYR A:401 , HOH A:543	BINDING SITE FOR RESIDUE MG A 403
04	AC4	SOFTWARE	ARG B:268 , ASP B:269 , ILE B:270 , HOH B:673	BINDING SITE FOR RESIDUE SO4 B 401
05	AC5	SOFTWARE	LYS B:98 , GLU C:135 , HOH C:693 , HOH C:723	BINDING SITE FOR RESIDUE NA B 402
06	AC6	SOFTWARE	CYS B:146 , ASN B:296 , HOH B:790	BINDING SITE FOR RESIDUE NA B 403
07	AC7	SOFTWARE	ALA B:108 , PRO B:139 , HOH B:629 , HOH B:798	BINDING SITE FOR RESIDUE GOL B 404
08	AC8	SOFTWARE	GLY B:30 , PRO B:31 , GLY B:32 , ASN B:33 , ILE B:34 , GLY B:55 , VAL B:56 , SER B:60 , ALA B:94 , THR B:95 , ALA B:99 , PRO B:119 , CYS B:146 , THR B:182 , ASN B:296 , LEU B:297 , HOH B:501 , HOH B:502 , HOH B:506 , HOH B:511 , HOH B:522 , HOH B:533 , HOH B:543 , HOH B:554 , HOH B:556 , HOH B:573 , HOH B:608 , HOH B:702 , HOH B:717 , HOH B:728 , HOH B:780 , HOH B:781 , HOH B:801	BINDING SITE FOR RESIDUE COA B 405
09	AC9	SOFTWARE	ARG C:21 , ASP C:22 , PHE C:143 , MET C:145 , VAL C:173 , SER C:175 , HIS C:204 , HIS C:206 , TYR C:295 , MG C:404 , HOH C:567	BINDING SITE FOR RESIDUE PYR C 401
10	BC1	SOFTWARE	ILE C:161 , ASP C:164 , HOH C:690 , HOH C:739 , HOH C:849	BINDING SITE FOR RESIDUE GOL C 402
11	BC2	SOFTWARE	HOH A:663 , HOH A:699 , PRO C:312 , ALA C:313 , HIS C:314 , HOH C:608	BINDING SITE FOR RESIDUE GOL C 403
12	BC3	SOFTWARE	ASP C:22 , HIS C:204 , HIS C:206 , PYR C:401 , HOH C:567	BINDING SITE FOR RESIDUE MG C 404
13	BC4	SOFTWARE	ASP A:183 , ARG A:187 , ARG D:251 , HOH D:632 , HOH D:743 , HOH D:797	BINDING SITE FOR RESIDUE SO4 D 401
14	BC5	SOFTWARE	CYS D:146 , ASN D:296 , HOH D:819	BINDING SITE FOR RESIDUE NA D 402
15	BC6	SOFTWARE	GLY D:30 , PRO D:31 , GLY D:32 , ASN D:33 , ILE D:34 , GLY D:55 , VAL D:56 , SER D:60 , ALA D:94 , THR D:95 , ALA D:99 , PRO D:119 , CYS D:146 , THR D:182 , ASN D:296 , LEU D:297 , HOH D:503 , HOH D:519 , HOH D:531 , HOH D:563 , HOH D:566 , HOH D:574 , HOH D:585 , HOH D:598 , HOH D:616 , HOH D:630 , HOH D:677 , HOH D:785 , HOH D:792 , HOH D:795 , HOH D:820	BINDING SITE FOR RESIDUE COA D 403

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

Asymmetric/Biological Unit

No.	Residues
1	Glu B:216	-	Pro B:217
2	Glu D:216	-	Pro D:217

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

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

(no "Exon" information available for 4LRT)

Asymmetric/Biological 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:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4lrta1 A:10-294 automated matches                                                                                                                                                                                                                                                           d4lrta2 A:295-343 automated matches               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeehhhhhhh....hhhhhhhhhhhhhhh...eeee..................hhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhh...eeeehhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lrt A  10 APRVRITDSTLRDGSHAMAHQFTEEQVRATVHALDAAGVEVIEVSHGDGLGGSSFNYGFSAVDEIDLVAAAVDEAVNAKIAVLLLPGVGTVRDLKRAHDAGASVARIATHCTEADVSCQHFAAARELGMETVGFLMLAHRIGPEELARQARIMVDAGAQCVYVVDSAGALVLSDVQARVQALVREIGHEAQVGFHGHQNLSLGVANSVLAYQNGARQIDGALCALGAGAGNSPTEILAATFERLNIETGVNVQAALAAAEEVVRPYLPRLPWADRAAIVQGYAGVYSSFLLHAERAAERYGVPAHEILQRVGEAGYVGGQEDMIIDIAVQLAEE 343
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339

Chain B from PDB  Type:PROTEIN  Length:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..hhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhh..eee.hhhhhhh.......eeee..hhhhhhhhhhhhhhhh.eeee..........hhhhhhhhhh...eee..hhhhhhhhhhhhhhhh......eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee.......eeeeeeeee....hhhhhhhhhhhhhhhhhh...eeee....eee..hhhhh..eeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lrt B  20 HMGKAVAAIVGPGNIGTDLLIKLQRSEHIEVRYMVGVDPASEGLARARKLGVEASAEGVDWLLEQDELPDLVFEATSAKAHLANAPRYAEAGITAIDLTPAAVGPLVCPPVNLTEHLDAPNVNMITCGGQATIPIVHAVSRVVPVAYAEIVAAIASRSAGPGTRANIDEFTETTAAAIEQVGGAARGKAIIILNPVEPPMIMRDTVYCAIPPDADTDAITASIEEMVAEVARYVPGYTLRTEPQYDQPRDIWKGMARVAVFLEVRGNGDYLPPWAGNLDIMTAAAARVGELLAQA 314
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309

Chain C from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4lrtc1 C:11-294 automated matches                                                                                                                                                                                                                                                          d4lrtc2 C:295-345 automated matches                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeehhhhhhh....hhhhhhhhhhhhhhhh..eeee..................hhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhh...eeeehhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lrt C  11 PRVRITDSTLRDGSHAMAHQFTEEQVRATVHALDAAGVEVIEVSHGDGLGGSSFNYGFSAVDEIDLVAAAVDEAVNAKIAVLLLPGVGTVRDLKRAHDAGASVARIATHCTEADVSCQHFAAARELGMETVGFLMLAHRIGPEELARQARIMVDAGAQCVYVVDSAGALVLSDVQARVQALVREIGHEAQVGFHGHQNLSLGVANSVLAYQNGARQIDGALCALGAGAGNSPTEILAATFERLNIETGVNVQAALAAAEEVVRPYLPRLPWADRAAIVQGYAGVYSSFLLHAERAAERYGVPAHEILQRVGEAGYVGGQEDMIIDIAVQLAEERH 345
                                    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       340

Chain D from PDB  Type:PROTEIN  Length:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhh..eee.hhhhhhhh......eeee..hhhhhhhhhhhhhhhh.eeee..........hhhhhhhhhh...eee..hhhhhhhhhhhhhhhh......eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee.......eeeeeeeee....hhhhhhhhhhhhhhhhhh....eee....eee..hhhhh..eeeeeeeee..........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lrt D  21 MGKAVAAIVGPGNIGTDLLIKLQRSEHIEVRYMVGVDPASEGLARARKLGVEASAEGVDWLLEQDELPDLVFEATSAKAHLANAPRYAEAGITAIDLTPAAVGPLVCPPVNLTEHLDAPNVNMITCGGQATIPIVHAVSRVVPVAYAEIVAAIASRSAGPGTRANIDEFTETTAAAIEQVGGAARGKAIIILNPVEPPMIMRDTVYCAIPPDADTDAITASIEEMVAEVARYVPGYTLRTEPQYDQPRDIWKGMARVAVFLEVRGNGDYLPPWAGNLDIMTAAAARVGELLAQ 313
                                    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

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: RuvA C-terminal domain-like (106)

Superfamily: post-HMGL domain-like (11)

Family: automated matches (3)

Protein domain: automated matches (3)

Thermomonospora curvata [TaxId: 471852] (2)

1a	d4lrta2	A:295-343
1b	d4lrtc2	C:295-345

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Aldolase (457)

Family: automated matches (113)

Protein domain: automated matches (113)

Thermomonospora curvata [TaxId: 471852] (2)

2a	d4lrta1	A:10-294
2b	d4lrtc1	C:11-294

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu B:216 - Pro B:217	[ RasMol ]
		Glu D:216 - Pro D:217	[ RasMol ]

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Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (6, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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