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(-) Description

Title :  CRYSTAL STRUCTURE OF AGROBACTERIUM TUMEFACIENS MALATE DEHYDROGENASE, NEW YORK STRUCTURAL GENOMICS CONSORTIUM
 
Authors :  Y. Patskovsky, S. C. Almo, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  08 Mar 05  (Deposition) - 15 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Malate Dehydrogenase, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, S. C. Almo
Crystal Structure Of Agrobacterium Tumefaciens Malate Dehydrogenase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Gene: AGR_L_3209
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 358

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:50 , HIS A:53 , HIS A:125 , PHE A:126 , GLY A:127 , PRO A:128 , ALA A:129 , CYS A:147 , THR A:165 , PRO A:167 , LEU A:182 , ASP A:183 , MET A:184 , ALA A:185 , PRO A:190 , MET A:315 , GLY A:318 , ARG A:320 , GLU A:321 , HOH A:769 , HOH A:810 , HOH A:835 , PHE B:235 , LYS B:236BINDING SITE FOR RESIDUE NAD A 700
2AC2SOFTWAREPHE A:235 , LYS A:236 , VAL B:50 , HIS B:53 , HIS B:125 , PHE B:126 , GLY B:127 , PRO B:128 , ALA B:129 , CYS B:147 , THR B:165 , PRO B:167 , LEU B:182 , ASP B:183 , MET B:184 , ALA B:185 , PRO B:190 , MET B:315 , GLY B:318 , ARG B:320 , GLU B:321 , HOH B:734 , HOH B:750 , HOH B:764 , HOH B:770 , HOH B:774 , HOH B:779 , HOH B:809 , HOH B:852BINDING SITE FOR RESIDUE NAD B 701
3AC3SOFTWAREVAL C:50 , HIS C:53 , HIS C:125 , PHE C:126 , GLY C:127 , PRO C:128 , ALA C:129 , CYS C:147 , THR C:165 , PRO C:167 , LEU C:182 , ASP C:183 , MET C:184 , ALA C:185 , PRO C:190 , MET C:315 , GLY C:318 , ARG C:320 , GLU C:321 , HOH C:756 , HOH C:795 , PHE D:235 , LYS D:236BINDING SITE FOR RESIDUE NAD C 702
4AC4SOFTWAREPHE C:235 , LYS C:236 , VAL D:50 , HIS D:53 , HIS D:125 , PHE D:126 , GLY D:127 , PRO D:128 , ALA D:129 , CYS D:147 , THR D:165 , PRO D:167 , LEU D:182 , ASP D:183 , MET D:184 , ALA D:185 , PRO D:190 , MET D:315 , GLY D:318 , ARG D:320 , GLU D:321 , HOH D:710 , HOH D:716 , HOH D:842BINDING SITE FOR RESIDUE NAD D 703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z2I)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:265 -Pro A:266
2Gly B:265 -Pro B:266
3Gly C:265 -Pro C:266
4Gly D:265 -Pro D:266

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z2I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z2I)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z2I)

(-) 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:350
 aligned with Q7CRW4_AGRFC | Q7CRW4 from UniProtKB/TrEMBL  Length:348

    Alignment length:350
                              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
         Q7CRW4_AGRFC     - --MARLDELERFCRAVFLAVGTDEETADAATRAMMHGTRLGVDSHGVRLLAHYVTALEGGRLNRRPQISRVSGFGAVETIDADHAHGARATYAAMENAMALAEKFGIGAVAIRNSSHFGPAGAYALEAARQGYIGLAFCNSDSFVRLHDGAMRFHGTNPIAVGVPAADDMPWLLDMATSAVPYNRVLLYRSLGQQLPQGVASDGDGVDTRDPNAVEMLAPVGGEFGFKGAALAGVVEIFSAVLTGMRLSFDLAPMGGPDFSTPRGLGAFVLALKPEAFLERDVFDESMKRYLEVLRGSPAREDCKVMAPGDREWAVAAKREREGAPVDPVTRAAFSELAEKFSVSPPTYH 348
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.........eeee....eeeee....hhhhhhhhhhhhhhhhhhhhheeeeeeeee.....hhhhhhhhhhh..eeeeee....................eeeee.......eeeee......hhhhhhhhhhh.......ee..............ee...hhhhhhhhhhhhhhhhhhhh......hhhhh.............eeeeeeee.hhhh.hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhh.....ee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z2i A   9 TVLARLDELERFCRAVFLAVGTDEETADAATRAMMHGTRLGVDSHGVRLLAHYVTALEGGRLNRRPQISRVSGFGAVETIDADHAHGARATYAAMENAMALAEKFGIGAVAIRNSSHFGPAGAYALEAARQGYIGLAFCNSDSFVRLHDGAMRFHGTNPIAVGVPAADDMPWLLDMATSAVPYNRVLLYRSLGQQLPQGVASDGDGVDTRDPNAVEMLAPVGGEFGFKGAALAGVVEIFSAVLTGMRLSFDLAPMGGPDFSTPRGLGAFVLALKPEAFLERDVFDESMKRYLEVLRGSPAREDCKVMAPGDREWAVAAKREREGAPVDPVTRAAFSELAEKFSVSPPTYH 358
                                    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       358


Chain B from PDB  Type:PROTEIN  Length:350
 aligned with Q7CRW4_AGRFC | Q7CRW4 from UniProtKB/TrEMBL  Length:348

    Alignment length:350
                              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
         Q7CRW4_AGRFC     - --MARLDELERFCRAVFLAVGTDEETADAATRAMMHGTRLGVDSHGVRLLAHYVTALEGGRLNRRPQISRVSGFGAVETIDADHAHGARATYAAMENAMALAEKFGIGAVAIRNSSHFGPAGAYALEAARQGYIGLAFCNSDSFVRLHDGAMRFHGTNPIAVGVPAADDMPWLLDMATSAVPYNRVLLYRSLGQQLPQGVASDGDGVDTRDPNAVEMLAPVGGEFGFKGAALAGVVEIFSAVLTGMRLSFDLAPMGGPDFSTPRGLGAFVLALKPEAFLERDVFDESMKRYLEVLRGSPAREDCKVMAPGDREWAVAAKREREGAPVDPVTRAAFSELAEKFSVSPPTYH 348
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.........eeee....eeeee....hhhhhhhhhhhhhhhhhhhhheeeeeeeee.....hhhhhhhhhhhh.eeeeee....................eeeee.......eeeee......hhhhhhhhhhh.......ee..............ee...hhhhhhhhhhhhhhhhhhhh......hhhhh.............eeeeeeee.hhhh.hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhh.....ee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z2i B   9 TVLARLDELERFCRAVFLAVGTDEETADAATRAMMHGTRLGVDSHGVRLLAHYVTALEGGRLNRRPQISRVSGFGAVETIDADHAHGARATYAAMENAMALAEKFGIGAVAIRNSSHFGPAGAYALEAARQGYIGLAFCNSDSFVRLHDGAMRFHGTNPIAVGVPAADDMPWLLDMATSAVPYNRVLLYRSLGQQLPQGVASDGDGVDTRDPNAVEMLAPVGGEFGFKGAALAGVVEIFSAVLTGMRLSFDLAPMGGPDFSTPRGLGAFVLALKPEAFLERDVFDESMKRYLEVLRGSPAREDCKVMAPGDREWAVAAKREREGAPVDPVTRAAFSELAEKFSVSPPTYH 358
                                    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       358


Chain C from PDB  Type:PROTEIN  Length:350
 aligned with Q7CRW4_AGRFC | Q7CRW4 from UniProtKB/TrEMBL  Length:348

    Alignment length:350
                              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
         Q7CRW4_AGRFC     - --MARLDELERFCRAVFLAVGTDEETADAATRAMMHGTRLGVDSHGVRLLAHYVTALEGGRLNRRPQISRVSGFGAVETIDADHAHGARATYAAMENAMALAEKFGIGAVAIRNSSHFGPAGAYALEAARQGYIGLAFCNSDSFVRLHDGAMRFHGTNPIAVGVPAADDMPWLLDMATSAVPYNRVLLYRSLGQQLPQGVASDGDGVDTRDPNAVEMLAPVGGEFGFKGAALAGVVEIFSAVLTGMRLSFDLAPMGGPDFSTPRGLGAFVLALKPEAFLERDVFDESMKRYLEVLRGSPAREDCKVMAPGDREWAVAAKREREGAPVDPVTRAAFSELAEKFSVSPPTYH 348
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.........eeee....eeeee....hhhhhhhhhhhhhhhhhhhhheeeeeeeee.....hhhhhhhhhhh..eeeeee....................eeeee.......eeeee......hhhhhhhhhhh.......ee..............ee...hhhhhhhhhhhhhhhhhhhh......hhhhh.............eeeeeeee.hhhh.hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhh.....ee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z2i C   9 TVLARLDELERFCRAVFLAVGTDEETADAATRAMMHGTRLGVDSHGVRLLAHYVTALEGGRLNRRPQISRVSGFGAVETIDADHAHGARATYAAMENAMALAEKFGIGAVAIRNSSHFGPAGAYALEAARQGYIGLAFCNSDSFVRLHDGAMRFHGTNPIAVGVPAADDMPWLLDMATSAVPYNRVLLYRSLGQQLPQGVASDGDGVDTRDPNAVEMLAPVGGEFGFKGAALAGVVEIFSAVLTGMRLSFDLAPMGGPDFSTPRGLGAFVLALKPEAFLERDVFDESMKRYLEVLRGSPAREDCKVMAPGDREWAVAAKREREGAPVDPVTRAAFSELAEKFSVSPPTYH 358
                                    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       358


Chain D from PDB  Type:PROTEIN  Length:350
 aligned with Q7CRW4_AGRFC | Q7CRW4 from UniProtKB/TrEMBL  Length:348

    Alignment length:350
                              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
         Q7CRW4_AGRFC     - --MARLDELERFCRAVFLAVGTDEETADAATRAMMHGTRLGVDSHGVRLLAHYVTALEGGRLNRRPQISRVSGFGAVETIDADHAHGARATYAAMENAMALAEKFGIGAVAIRNSSHFGPAGAYALEAARQGYIGLAFCNSDSFVRLHDGAMRFHGTNPIAVGVPAADDMPWLLDMATSAVPYNRVLLYRSLGQQLPQGVASDGDGVDTRDPNAVEMLAPVGGEFGFKGAALAGVVEIFSAVLTGMRLSFDLAPMGGPDFSTPRGLGAFVLALKPEAFLERDVFDESMKRYLEVLRGSPAREDCKVMAPGDREWAVAAKREREGAPVDPVTRAAFSELAEKFSVSPPTYH 348
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh........eeee....eeeee....hhhhhhhhhhhhhhhhhhhhheeeeeeeee.....hhhhhhhhhhhh.eeeeee....................eeeee.......eeeee......hhhhhhhhhhh.......ee..............ee...hhhhhhhhhhhhhhhhhhhh......hhhhh.............eeeeeeee.hhhh.hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhh.....ee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z2i D   9 TVLARLDELERFCRAVFLAVGTDEETADAATRAMMHGTRLGVDSHGVRLLAHYVTALEGGRLNRRPQISRVSGFGAVETIDADHAHGARATYAAMENAMALAEKFGIGAVAIRNSSHFGPAGAYALEAARQGYIGLAFCNSDSFVRLHDGAMRFHGTNPIAVGVPAADDMPWLLDMATSAVPYNRVLLYRSLGQQLPQGVASDGDGVDTRDPNAVEMLAPVGGEFGFKGAALAGVVEIFSAVLTGMRLSFDLAPMGGPDFSTPRGLGAFVLALKPEAFLERDVFDESMKRYLEVLRGSPAREDCKVMAPGDREWAVAAKREREGAPVDPVTRAAFSELAEKFSVSPPTYH 358
                                    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       358
   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  (0, 0)

(no "SCOP Domain" information available for 1Z2I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Z2I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Z2I)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q7CRW4_AGRFC | Q7CRW4)
molecular function
    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.
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.

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