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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINO ACID-BINDING ACT: D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE CATALYTIC DOMAIN FROM BRUCELLA MELITENSIS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  07 Oct 09  (Deposition) - 03 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Niaid, Ssgcid, Seattle Structural Genomics Center For Infectious Disease, Brucellosis, Coccobacillus, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. E. Edwards, J. Abendroth, E. R. Smith, Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of Amino Acid-Binding Act: D-Isomer Specific 2-Hydroxyacid Dehydrogenase Catalytic Domain From Brucella Melitensis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - D-3-PHOSPHOGLYCERATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.95
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: AVA0421
    Gene: BMEII0813
    Mutation: YES
    Organism Scientific: BRUCELLA MELITENSIS BIOVAR ABORTUS
    Organism Taxid: 359391
    Strain: BIOVAR ABORTUS 2308

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GOL3Ligand/IonGLYCEROL
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2GOL12Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:148 , ASP A:206 , LYS A:231 , LYS A:232 , GLY A:233BINDING SITE FOR RESIDUE EDO A 413
2AC2SOFTWAREASP A:182 , THR A:183 , VAL A:212 , PRO A:213BINDING SITE FOR RESIDUE GOL A 414
3AC3SOFTWAREPHE A:107 , SER A:108 , THR A:110 , ARG A:111 , ARG A:151 , GLN A:166 , ARG A:304BINDING SITE FOR RESIDUE GOL A 415
4AC4SOFTWAREARG A:336 , THR A:338 , GLY A:339 , THR A:340 , ARG A:341 , GLU A:384 , TYR A:412BINDING SITE FOR RESIDUE GOL A 416

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K5P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K5P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K5P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K5P)

(-) Exons   (0, 0)

(no "Exon" information available for 3K5P)

(-) 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:400
 aligned with Q2YK82_BRUA2 | Q2YK82 from UniProtKB/TrEMBL  Length:412

    Alignment length:405
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407     
         Q2YK82_BRUA2     8 SRDRINVLLLEGISQTAVEYFKSSGYTNVTHLPKALDKADLIKAISSAHIIGIRSRTQLTEEIFAAANRLIAVGCFSVGTNQVELKAARKRGIPVFNAPFSNTRSVAELVIGEIIMLMRRIFPRSVSAHAGGWEKTAIGSREVRGKTLGIVGYGNIGSQVGNLAESLGMTVRYYDTSDKLQYGNVKPAASLDELLKTSDVVSLHVPSSKSTSKLITEAKLRKMKKGAFLINNARGSVVDLEALAKVLQEGHLAGAAIDVFPVEPASNGERFSTPLQGLENVILTPHIGGSTEEAQERIGTEVTRKLVEYSDVGSTVGAVNFPQVQLPPRPTGTRFMHVHENRPGILNSLMNVFSHHHINIASQFLQTDGEVGYLVMEADGVGEASDAVLQEIREIPGTIRARLLY 412
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3k5pA01 A:8-109,A:299-327 NAD(P)-binding Rossmann-like Domain                                         3k5pA02 A:110-298 NAD(P)-binding Rossmann-like Domain                                                                                                                                        3k5pA01 A:8-109,A:299-327    -3k5pA03 A:329-411  [code=3.30.70.260, no name defined]                             - CATH domains
           Pfam domains (1) ------2-Hacid_dh-3k5pA02 A:14-327                                                                                                                                                                                                                                                                                               ------------ACT-3k5pA01 A:340-404                                            -------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------2-Hacid_dh_C-3k5pA03 A:118-295                                                                                                                                                    --------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhh.eee....hhhhhhhhhhh....eee.....hhhhhhhhhh...eeee......hhhhhhhh....eeee........hhhhhhhh...ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................eeeee..hhhhhhhhhhhhhh..eeeee...........ee..hhhhhhhhh.eeee....-----...hhhhhhhh...eeeee.......hhhhhhhhhhh..eeeeee.......................eee.......hhhhhhhhhhhhhhhhhhhhhhh...................eeeeeee....hhhhhhhhhhhhh...eeeeeeee....eeeeeee..hhhhhhhhhhhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k5p A   8 SRDRINVLLLEGISQTAVEYFKSSGYTNVTHLPKALDKADLIKAISSAHIIGIRSRTQLTEEIFAAANRLIAVGCFSVGTNQVELKAARKRGIPVFNAPFSNTRSVAELVIGEIIMLMRRIFPRSVSAHAGGWEKTAIGSREVRGKTLGIVGYGNIGSQVGNLAESLGMTVRYYDTSDKLQYGNVKPAASLDELLKTSDVVSLHVPS-----KLITEAKLRKMKKGAFLINNARGSDVDLEALAKVLQEGHLAGAAIDVFPVEPASNGERFSTPLQGLENVILTPHIGGSTEEAQERIGTEVTRKLVEYSDVGSTVGAVNFPQVQLPPRPTGTRFMHVHENRPGILNSLMNVFSHHHINIASQFLQTDGEVGYLVMEADGVGEASDAVLQEIREIPGTIRARLLY 412
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207      |  -  |    227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407     
                                                                                                                                                                                                                                        214   220
   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  (0, 0)

(no "SCOP Domain" information available for 3K5P)

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: ACT (34)
(-)
Clan: Form_Glyc_dh (56)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q2YK82_BRUA2 | Q2YK82)
molecular function
    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:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    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:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
    GO:0004617    phosphoglycerate dehydrogenase activity    Catalysis of the reaction: 3-phosphoglycerate + NAD+ = 3-phosphohydroxypyruvate + NADH + H+.
biological process
    GO:0006564    L-serine biosynthetic process    The chemical reactions and pathways resulting in the formation of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    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.

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