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(-) Description

Title :  CRYSTAL STRUCTURE OF ALANINE DEHYDROGENASE/PYRIDINE NUCLEOTIDE TRANSHYDROGENASE FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  04 Oct 10  (Deposition) - 13 Oct 10  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Tuberculosis, Non-Pathogenic Species, Ortholog, Dehydrogenase, Pyruvate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
PubMed-ID: 25613812  |  Reference-DOI: 10.1016/J.TUBE.2014.12.003

(-) Compounds

Molecule 1 - ALANINE DEHYDROGENASE/PYRIDINE NUCLEOTIDE TRANSHYDROGENASE
    Chains: A
    EC Number: 1.4.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: AVA0421
    Gene: MSMEG_0152
    Organism Scientific: MYCOBACTERIUM SMEGMATIS STR. MC2 155
    Organism Taxid: 246196
    Strain: ATCC 700084 / MC(2)155

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3NA-1Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:1 , HOH A:701 , HOH A:702 , HOH A:703BINDING SITE FOR RESIDUE CA A 361
2AC2SOFTWAREGLY A:55 , HOH A:557 , HOH A:571 , HOH A:707BINDING SITE FOR RESIDUE CA A 362
3AC3SOFTWAREASP A:331 , LEU A:334 , HOH A:503 , HOH A:671BINDING SITE FOR RESIDUE CA A 363
4AC4SOFTWARELYS A:244 , HOH A:533 , HOH A:556 , HOH A:579 , HOH A:600 , HOH A:720BINDING SITE FOR RESIDUE NA A 364
5AC5SOFTWAREGLY A:294 , ARG A:295 , THR A:296 , THR A:305 , HOH A:516 , HOH A:696BINDING SITE FOR RESIDUE EDO A 365
6AC6SOFTWARELYS A:138 , LEU A:142 , SER A:145 , LEU A:310 , HOH A:388 , HOH A:434BINDING SITE FOR RESIDUE EDO A 366

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P2Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P2Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P2Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P2Y)

(-) Exons   (0, 0)

(no "Exon" information available for 3P2Y)

(-) 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:345
 aligned with A0QNT0_MYCS2 | A0QNT0 from UniProtKB/TrEMBL  Length:360

    Alignment length:358
                              1                                                                                                                                                                                                                                                                                                                                                                   
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348        
         A0QNT0_MYCS2     - --MTLIGVPRESAEGERRVALVPKVVEKLSARGLEVVVESAAGAGALFSDADYERAGATIGDPWPADVVVKVNPPTSDEISQLKPGSVLIGFLAPRTQPELASRLRIADVTAFAMESIPRISRAQTMDALSSQANVAGYKAVLLGASLSTRFVPMLTTAAGTVKPASALVLGVGVAGLQALATAKRLGAKTTGYDVRPEVAEQVRSVGAQWLDLGIDAAGEGGYARELSEAERAQQQQALEDAITKFDIVITTALVPGRPAPRLVTAAAATGMQPGSVVVDLAGETGGNCELTEPGRTIVHHGVTITSPLNLPATMPEHASELYAKNVTALLDLLLTDDGVAPDFTDEIVAASCITRT 356
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------AlaDh_PNT_N-3p2yA01 A:5-135                                                                                                        --------AlaDh_PNT_C-3p2yA02 A:144-306                                                                                                                                      -------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.............hhhhhhhhhhh..eeee....hhhhh.hhhhhhhh..ee.......eee.....hhhhhh......eeee......hhhhhhhhhhh..eeee.hhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee....ee...eeeee..hhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhh..ee....-------------hhhhhhhhhhhhhhhhh...eeee.............hhhhhhh.....eeee.hhhhh..........eeee..eeee....hhhhhhhhhhhhhhhhhhhhhhhhee..ee.....hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p2y A  -1 GSMTLIGVPRESAEGERRVALVPKVVEKLSARGLEVVVESAAGAGALFSDADYERAGATIGDPWPADVVVKVNPPTSDEISQLKPGSVLIGFLAPRTQPELASRLRIADVTAFAMESIPRISRAQTMDALSSQANVAGYKAVLLGASLSTRFVPMLTTAAGTVKPASALVLGVGVAGLQALATAKRLGAKTTGYDVRPEVAEQVRSVGAQWLDLG-------------SEAERAQQQQALEDAITKFDIVITTALVPGRPAPRLVTAAAATGMQPGSVVVDLAGETGGNCELTEPGRTIVHHGVTITSPLNLPATMPEHASELYAKNVTALLDLLLTDDGVAPDFTDEIVAASCITRT 356
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208    |    -       228       238       248       258       268       278       288       298       308       318       328       338       348        
                                                                                                                                                                                                                                                213           227
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3P2Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P2Y)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Form_Glyc_dh (56)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (A0QNT0_MYCS2 | A0QNT0)
molecular function
    GO:0008750    NAD(P)+ transhydrogenase (AB-specific) activity    Catalysis of the reaction: NADPH + H+ + NAD+ = NADP+ + NADH + H+. The reaction is A-specific (i.e. the pro-R hydrogen is transferred from the 4-position of reduced nicotinamide cofactor) with respect to NAD+ and B-specific (i.e. the pro-S hydrogen is transferred) with respect to NADP+.
    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.
biological process
    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.

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