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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ALDEHYDE DEHYDROGENASE COMPLEXED WITH NAD+
 
Authors :  J. H. Moon, A. E. Lyon, M. Yu, L-W. Hung, T. Terwilliger, C-Y. Kim, Integr Center For Structure And Function Innovation (Isfi), Tb Stru Genomics Consortium (Tbsgc)
Date :  24 Oct 07  (Deposition) - 27 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rv0223C-Nad Complex, Structural Genomics, Psi-2, Protein Structure Initiative, Integrated Center For Structure And Function Innovation, Isfi, Tb Structural Genomics Consortium, Tbsgc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Moon, A. E. Lyon, M. Yu, L-W. Hung, T. Terwilliger, C-Y. Kim
X-Ray Crystal Structure Of Aldehyde Dehydrogenase From Mycobacterium Tuberculosis Complexed With Nad+.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALDEHYDE DEHYDROGENASE
    Atcc: 25618
    Chains: A
    EC Number: 1.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RV0223C, MT0233
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1EOH3Ligand/IonETHANOL
2GOL4Ligand/IonGLYCEROL
3NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (4, 20)
No.NameCountTypeFull Name
1EOH6Ligand/IonETHANOL
2GOL8Ligand/IonGLYCEROL
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4SO44Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:235 , ARG A:238 , HOH A:807 , HOH A:925 , HOH A:1105BINDING SITE FOR RESIDUE SO4 A 801
02AC2SOFTWAREARG A:242 , ARG A:243BINDING SITE FOR RESIDUE SO4 A 802
03AC3SOFTWAREILE A:153 , VAL A:154 , ALA A:155 , TRP A:156 , ASN A:157 , LYS A:180 , ALA A:182 , ILE A:213 , GLY A:216 , PHE A:230 , THR A:231 , GLY A:232 , SER A:233 , VAL A:236 , GLU A:239 , GLU A:254 , LEU A:255 , GLY A:256 , CYS A:288 , GLU A:387 , PHE A:389 , PHE A:452 , GOL A:602 , HOH A:855 , HOH A:899 , HOH A:947 , HOH A:1120 , HOH A:1141BINDING SITE FOR RESIDUE NAD A 500
04AC4SOFTWAREASP A:268 , ARG A:298 , HOH A:1168 , HOH A:1192 , HOH A:1207BINDING SITE FOR RESIDUE GOL A 600
05AC5SOFTWAREASP A:302 , VAL A:305 , ALA A:306 , PRO A:316 , GLN A:326 , ARG A:352 , HOH A:870BINDING SITE FOR RESIDUE GOL A 601
06AC6SOFTWAREASN A:157 , PHE A:161 , GLY A:287 , CYS A:288 , NAD A:500 , HOH A:899 , HOH A:1225BINDING SITE FOR RESIDUE GOL A 602
07AC7SOFTWAREMET A:227 , PRO A:250 , GLY A:461 , HIS A:471 , THR A:473 , GLN A:474 , HOH A:850 , HOH A:1062 , HOH A:1125BINDING SITE FOR RESIDUE GOL A 603
08AC8SOFTWARECYS A:30 , PRO A:320BINDING SITE FOR RESIDUE EOH A 701
09AC9SOFTWAREVAL A:267 , ASP A:268 , LEU A:269 , ALA A:270 , ARG A:300BINDING SITE FOR RESIDUE EOH A 702
10BC1SOFTWAREASN A:379 , ILE A:407 , ASP A:410 , HOH A:934BINDING SITE FOR RESIDUE EOH A 703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B4W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3B4W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B4W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B4W)

(-) Exons   (0, 0)

(no "Exon" information available for 3B4W)

(-) 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:483
 aligned with P96405_MYCTO | P96405 from UniProtKB/TrEMBL  Length:487

    Alignment length:483
                                    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       353       363       373       383       393       403       413       423       433       443       453       463       473       483   
         P96405_MYCTO     4 SATEYDKLFIGGKWTKPSTSDVIEVRCPATGEYVGKVPMAAAADVDAAVAAARAAFDNGPWPSTPPHERAAVIAAAVKMLAERKDLFTKLLAAETGQPPTIIETMHWMGSMGAMNYFAGAADKVTWTETRTGSYGQSIVSREPVGVVGAIVAWNVPLFLAVNKIAPALLAGCTIVLKPAAETPLTANALAEVFAEVGLPEGVLSVVPGGIETGQALTSNPDIDMFTFTGSSAVGREVGRRAAEMLKPCTLELGGKSAAIILEDVDLAAAIPMMVFSGVMNAGQGCVNQTRILAPRSRYDEIVAAVTNFVTALPVGPPSDPAAQIGPLISEKQRTRVEGYIAKGIEEGARLVCGGGRPEGLDNGFFIQPTVFADVDNKMTIAQEEIFGPVLAIIPYDTEEDAIAIANDSVYGLAGSVWTTDVPKGIKISQQIRTGTYGINWYAFDPGSPFGGYKNSGIGRENGPEGVEHFTQQKSVLLPMGYTV 486
               SCOP domains d3b4wa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3b4wA01 A:4-256,A:448-486 Aldehyde Dehydrogenase; Chain A, domain 1                                                                                                                                                                                          3b4wA02 A:257-447 Aldehyde Dehydrogenase; Chain A, domain 2                                                                                                                                    3b4wA01 A:4-256,A:448-486               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...eee..eee......eeeee......eeeeee..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeee..eeeeeeeee..eeeee....hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh......eee...hhhhhhhhh......eeeee.hhhhhhhhhhhhhhh...eeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh..eeee................eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh.......eee..hhhhhhhhhhhh.....ee.............hhh.ee...hhhhhhhh.eeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b4w A   4 SATEYDKLFIGGKWTKPSTSDVIEVRCPATGEYVGKVPMAAAADVDAAVAAARAAFDNGPWPSTPPHERAAVIAAAVKMLAERKDLFTKLLAAETGQPPTIIETMHWMGSMGAMNYFAGAADKVTWTETRTGSYGQSIVSREPVGVVGAIVAWNVPLFLAVNKIAPALLAGCTIVLKPAAETPLTANALAEVFAEVGLPEGVLSVVPGGIETGQALTSNPDIDMFTFTGSSAVGREVGRRAAEMLKPCTLELGGKSAAIILEDVDLAAAIPMMVFSGVMNAGQGCVNQTRILAPRSRYDEIVAAVTNFVTALPVGPPSDPAAQIGPLISEKQRTRVEGYIAKGIEEGARLVCGGGRPEGLDNGFFIQPTVFADVDNKMTIAQEEIFGPVLAIIPYDTEEDAIAIANDSVYGLAGSVWTTDVPKGIKISQQIRTGTYGINWYAFDPGSPFGGYKNSGIGRENGPEGVEHFTQQKSVLLPMGYTV 486
                                    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       353       363       373       383       393       403       413       423       433       443       453       463       473       483
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B4W)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (P96405_MYCTO | P96405)
molecular function
    GO:0043531    ADP binding    Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
    GO:0016208    AMP binding    Interacting selectively and non-covalently with AMP, adenosine monophosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0071949    FAD binding    Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0070404    NADH binding    Interacting selectively and non-covalently with the reduced form, NADH, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016620    oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  3b4w
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