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(-) Description

Title :  CRYSTAL STRUCTURE OF TM1643
 
Authors :  Z. Yang, A. Savchenko, A. Edwards, C. Arrowsmith, L. Tong, Northeast S Genomics Consortium (Nesg)
Date :  08 Aug 02  (Deposition) - 15 Aug 02  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Unknown Function, Possible Nad-Dependent Oxidoreductase, Psi, Protein Structure Initiative, Nesg, Northeast Structural Genomics Consortium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Yang, A. Savchenko, A. Yakunin, R. Zhang, A. Edwards, C. Arrowsmith L. Tong
Aspartate Dehydrogenase, A Novel Enzyme Identified From Structural And Functional Studies Of Tm1643
J. Biol. Chem. V. 278 8804 2003
PubMed-ID: 12496312  |  Reference-DOI: 10.1074/JBC.M211892200

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN TM1643
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:7 , GLY A:9 , ASN A:10 , ILE A:11 , ASP A:28 , ARG A:29 , ILE A:30 , ALA A:56 , SER A:57 , PRO A:58 , ALA A:60 , GLU A:63 , TYR A:64 , ILE A:78 , SER A:79 , GLY A:108 , ALA A:109 , ASN A:164 , THR A:223 , HOH A:2002BINDING SITE FOR RESIDUE NAD A 1242

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H2H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1H2H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H2H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1H2H)

(-) Exons   (0, 0)

(no "Exon" information available for 1H2H)

(-) 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:233
 aligned with ASPD_THEMA | Q9X1X6 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 
           ASPD_THEMA     1 MTVLIIGMGNIGKKLVELGNFEKIYAYDRISKDIPGVVRLDEFQVPSDVSTVVECASPEAVKEYSLQILKNPVNYIIISTSAFADEVFRERFFSELKNSPARVFFPSGAIGGLDVLSSIKDFVKNVRIETIKPPKSLGLDLKGKTVVFEGSVEEASKLFPRNINVASTIGLIVGFEKVKVTIVADPAMDHNIHIVRISSAIGNYEFKIENIPSPENPKTSMLTVYSILRTLRNLESKIIFG 241
               SCOP domains d1h2ha4 A:1-108,A:220-241 Hypothetical protein TM1643                                                       d1h2ha3 A:109-211 Hypothetical protein TM1643                                                          --------d1h2ha4                SCOP domains
               CATH domains -1h2hA01 A:2-108,A:220-241 NAD(P)-binding Rossmann-like Domain                                              1h2hA02 A:109-211 Dihydrodipicolinate Reductase; domain 2                                              --------1h2hA01                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhh...eeeee..........ee...........eeee..hhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhhhh..eee.......hhhhhhhh...eeeeeeeeeehhhhhh......eeeeeehhhhhhhhh....hhhhhhhhhhh...eeeeeee.......eeeeeeee...eeeeee...--------hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h2h A   1 mTVLIIGmGNIGKKLVELGNFEKIYAYDRISKDIPGVVRLDEFQVPSDVSTVVECASPEAVKEYSLQILKNPVNYIIISTSAFADEVFRERFFSELKNSPARVFFPSGAIGGLDVLSSIKDFVKNVRIETIKPPKSLGLDLKGKTVVFEGSVEEASKLFPRNINVASTIGLIVGFEKVKVTIVADPAmDHNIHIVRISSAIGNYEFKIENI--------SmLTVYSILRTLRNLESKIIFG 241
                            |      |10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210|      220|      230       240 
                            |      8-MSE                                                                                                                                                                             188-MSE                211      220|                    
                            1-MSE                                                                                                                                                                                                                     221-MSE
   Legend:   → Mismatch (orange background)
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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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
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 1H2H)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (ASPD_THEMA | Q9X1X6)
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:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0033735    aspartate dehydrogenase activity    Catalysis of the reaction: L-aspartate + H2O + NAD(P)+ = oxaloacetate + NH3 + NAD(P)H + H+.
    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:0016639    oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0009435    NAD biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
    GO:0006742    NADP catabolic process    The chemical reactions and pathways resulting in the breakdown of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; catabolism may be of either the oxidized form, NADP, or the reduced form, NADPH.
    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.
    GO:0019363    pyridine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.

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 Related Entries

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        ASPD_THEMA | Q9X1X6: 1j5p

(-) Related Entries Specified in the PDB File

1j5p CRYSTAL STRUCTURE OF CONSERVED HYPOTHETICAL PROTEIN (TM1643)FROM THERMOTOGA MARITIMA AT 1.9 A RESOLUTION
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