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(-) Description

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 :  1.55
Chains :  Asym. Unit :  A,B,N
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  N  (1x)
Keywords :  Rossmann Fold, Tim Barrel Domain, Dehydrogenase, Aldolase, Oxidoreductase (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
PubMed: search

(-) Compounds

Molecule 1 - 4-HYDROXY-2-OXOVALERATE ALDOLASE
    Chains: A
    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
    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]
 
Molecule 3 - SYMMETRIC ALDOLASE, C-TERMINAL DISORDERED RESIDUES
    Chains: N
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: C41 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOMONOSPORA CURVATA
    Organism Taxid: 2020
    Strain: DSM 43183

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABN
Biological Unit 1 (2x): AB 
Biological Unit 2 (1x):   N

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 20)

Asymmetric Unit (8, 20)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FOR1Mod. ResidueFORMYL GROUP
3GOL6Ligand/IonGLYCEROL
4MG1Ligand/IonMAGNESIUM ION
5NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
6PEG7Ligand/IonDI(HYDROXYETHYL)ETHER
7PYR1Ligand/IonPYRUVIC ACID
8SO41Ligand/IonSULFATE ION
Biological Unit 1 (6, 34)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FOR2Mod. ResidueFORMYL GROUP
3GOL12Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
6PEG14Ligand/IonDI(HYDROXYETHYL)ETHER
7PYR2Ligand/IonPYRUVIC ACID
8SO42Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FOR-1Mod. ResidueFORMYL GROUP
3GOL-1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5NAD-1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
6PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
7PYR-1Ligand/IonPYRUVIC ACID
8SO4-1Ligand/IonSULFATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:151 , PRO A:152 , GLU A:153 , GLU A:154 , HOH A:554 , HOH A:677BINDING SITE FOR RESIDUE SO4 A 401
02AC2SOFTWAREARG A:21 , ASP A:22 , PHE A:143 , MET A:145 , VAL A:173 , SER A:175 , HIS A:204 , HIS A:206 , TYR A:295 , MG A:404 , HOH A:547BINDING SITE FOR RESIDUE PYR A 402
03AC3SOFTWARESER A:182 , GLN A:221 , HOH A:642BINDING SITE FOR RESIDUE CL A 403
04AC4SOFTWAREASP A:22 , HIS A:204 , HIS A:206 , PYR A:402 , HOH A:547BINDING SITE FOR RESIDUE MG A 404
05AC5SOFTWAREASP A:183 , ARG A:252 , LEU A:253BINDING SITE FOR RESIDUE GOL A 405
06AC6SOFTWAREHIS A:107 , GLY A:110 , ALA A:111 , SER A:112 , GLY A:137 , HOH A:711BINDING SITE FOR RESIDUE PEG A 406
07AC7SOFTWAREPRO A:274 , PEG A:409 , HOH A:604 , HOH A:742 , HOH A:752BINDING SITE FOR RESIDUE PEG A 407
08AC8SOFTWAREVAL A:85 , GLN A:262 , ALA A:263 , PEG A:410 , HOH A:708 , HOH A:730 , HOH A:734BINDING SITE FOR RESIDUE PEG A 408
09AC9SOFTWAREGLU A:270 , PEG A:407 , HOH A:750 , HOH A:752 , HOH A:777BINDING SITE FOR RESIDUE PEG A 409
10BC1SOFTWAREALA A:42 , ALA A:263 , ALA A:266 , ALA A:267 , GLU A:270 , VAL A:271 , PEG A:408 , HOH A:631BINDING SITE FOR RESIDUE PEG A 410
11BC2SOFTWAREVAL B:29 , GLY B:30 , PRO B:31 , GLY B:32 , ASN B:33 , ILE B:34 , GLY B:55 , VAL B:56 , ALA B:94 , THR B:95 , SER B:96 , LEU B:117 , THR B:118 , PRO B:119 , CYS B:146 , SER B:177 , GLY B:179 , PRO B:180 , GLY B:181 , THR B:182 , ASN B:185 , ASN B:296 , LEU B:297 , PEG B:409 , HOH B:507 , HOH B:524 , HOH B:537 , HOH B:548 , HOH B:566 , HOH B:571 , HOH B:619 , HOH B:673 , HOH B:713 , HOH B:761BINDING SITE FOR RESIDUE NAD B 401
12BC3SOFTWARETHR B:260 , GLU B:261 , PRO B:262 , VAL B:279 , PHE B:280BINDING SITE FOR RESIDUE CL B 402
13BC4SOFTWAREGLU B:61 , ALA B:233 , ASP B:234 , THR B:235 , GOL B:405 , HOH B:587 , HOH B:590 , HOH B:609BINDING SITE FOR RESIDUE GOL B 403
14BC5SOFTWAREARG B:268 , ASP B:269 , ILE B:270BINDING SITE FOR RESIDUE GOL B 404
15BC6SOFTWAREGLU B:61 , PRO B:231 , THR B:235 , TYR B:264 , ASP B:265 , GLN B:266 , PRO B:267 , ALA B:275 , ARG B:276 , GOL B:403 , HOH B:567BINDING SITE FOR RESIDUE GOL B 405
16BC7SOFTWARETHR B:257 , LEU B:258 , ARG B:259 , HOH B:680BINDING SITE FOR RESIDUE GOL B 406
17BC8SOFTWAREPRO B:231 , GLY B:287 , TYR B:289 , LEU B:290 , PRO B:291 , HOH B:684 , HOH B:706BINDING SITE FOR RESIDUE GOL B 407
18BC9SOFTWAREVAL B:162 , PRO B:163 , PRO B:230 , ALA B:233 , ASP B:234 , HOH B:560BINDING SITE FOR RESIDUE PEG B 408
19CC1SOFTWAREPRO B:180 , GLY B:181 , NAD B:401 , HOH B:621 , HOH B:673 , ALA N:156 , HOH N:201BINDING SITE FOR RESIDUE PEG B 409
20CC2SOFTWAREHIS A:119 , HOH A:521 , LEU B:212 , HOH B:510BINDING SITE FOR RESIDUE FOR B 410
21CC3SOFTWAREHOH A:785 , PRO B:180 , PEG B:409 , HOH N:201BINDING SITE FOR CHAIN N OF SYMMETRIC ALDOLASE, C-TERMINAL DISORDERED RESIDUES

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu B:216 -Pro B:217

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LRS)

(-) Sequences/Alignments

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:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4lrsa1 A:10-294 automated matches                                                                                                                                                                                                                                                           d4lrsa2 A:295-346 automated matches                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....hhhhhh.....hhhhhhhhhhhhhh...eee....................hhhhhhhhhhh....eeeeee......hhhhhhhhhh...eeeeeee......hhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhh...eeee.............hhhhhhhhhhh.......hhhhhhhhhhh............hhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhh......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lrs A  10 APRVRITDSTLRDGSHAMAHQFTEEQVRATVHALDAAGVEVIEVSHGDGLGGSSFNYGFSAVDEIDLVAAAVDEAVNAKIAVLLLPGVGTVRDLKRAHDAGASVARIATHCTEADVSCQHFAAARELGMETVGFLMLAHRIGPEELARQARIMVDAGAQCVYVVDSAGALVLSDVQARVQALVREIGHEAQVGFHGHQNLSLGVANSVLAYQNGARQIDGALCALGAGAGNSPTEILAATFERLNIETGVNVQAALAAAEEVVRPYLPRLPWADRAAIVQGYAGVYSSFLLHAERAAERYGVPAHEILQRVGEAGYVGGQEDMIIDIAVQLAEERHG 346
                                    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:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhh...eeeeeee......hhhhhhhhh..eee.hhhhhhhh......eeee...hhhhhhhhhhhhhh..eeee.......................eee...hhhhhhhhhhhhhhh.....eeeeeeeee.....hhhhh.hhhhhhhhhhhhhhh....eeeeeeeee........eeeeeeee.....hhhhhhhhhhhhhhhhh....eee....eee.........eeeeeeeee...........hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lrs B  22 GKAVAAIVGPGNIGTDLLIKLQRSEHIEVRYMVGVDPASEGLARARKLGVEASAEGVDWLLEQDELPDLVFEATSAKAHLANAPRYAEAGITAIDLTPAAVGPLVCPPVNLTEHLDAPNVNMITCGGQATIPIVHAVSRVVPVAYAEIVAAIASRSAGPGTRANIDEFTETTAAAIEQVGGAARGKAIIILNPVEPPMIMRDTVYCAIPPDADTDAITASIEEMVAEVARYVPGYTLRTEPQYDQPRDIWKGMARVAVFLEVRGNGDYLPPWAGNLDIMTAAAARVGELLAQAP 315
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311    


Chain N from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 4lrs N 156 AAA 158
   Legend:   → Mismatch (orange background)
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    → 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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 14)

Asymmetric Unit(hide GO term definitions)

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  4lrs
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4lrt