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(-) Description

Title :  STRUCTURE OF PUTATIVE LACTATE DEHYDROGENASE FROM FRANCISELLA TULARENSIS SUBSP. TULARENSIS SCHU S4
 
Authors :  T. Osinski, M. Cymborowski, M. D. Zimmerman, E. Gordon, S. Grimshaw, T. M. Chruszcz, A. Savchenko, W. Anderson, W. Minor, Center For Struct Genomics Of Infectious Diseases (Csgid)
Date :  12 Oct 10  (Deposition) - 20 Oct 10  (Release) - 20 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Putative Dehydrogenase, Enzyme, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Osinski, M. Cymborowski, M. D. Zimmerman, E. Gordon, S. Grimshaw, T. Skarina, M. Chruszcz, A. Savchenko, W. Anderson, W. Minor
Structure Of Putative Lactate Dehydrogenase From Francisell Tularensis Subsp. Tularensis Schu S4
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FTT_0535C, MDH
    Organism Scientific: FRANCISELLA TULARENSIS
    Organism Taxid: 119856
    Strain: TULARENSIS

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 54)

Asymmetric/Biological Unit (2, 54)
No.NameCountTypeFull Name
1MSE52Mod. Amino AcidSELENOMETHIONINE
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY C:266 , LEU C:267 , ASP C:268 , ARG C:296 , GLN C:300 , ILE C:303 , LYS C:307BINDING SITE FOR RESIDUE PO4 C 320
2AC2SOFTWARETHR D:184 , GLU D:195 , SER D:292 , LYS D:294 , GLU D:295 , HOH D:374BINDING SITE FOR RESIDUE PO4 D 320

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P7M)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Pro A:85 -Gly A:86
2Asn A:121 -Pro A:122
3Pro B:85 -Gly B:86
4Asn B:121 -Pro B:122
5Pro C:85 -Gly C:86
6Asn C:121 -Pro C:122
7Asn D:121 -Pro D:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P7M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P7M)

(-) Exons   (0, 0)

(no "Exon" information available for 3P7M)

(-) Sequences/Alignments

Asymmetric/Biological 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:318
 aligned with Q8G942_FRATL | Q8G942 from UniProtKB/TrEMBL  Length:319

    Alignment length:318
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310        
         Q8G942_FRATL     1 MARKKITLVGAGNIGGTLAHLALIKQLGDVVLFDIAQGMPNGKALDLLQTCPIEGVDFKVRGTNDYKDLENSDVVIVTAGVPRKPGMSRDDLLGINIKVMQTVGEGIKHNCPNAFVICITNPLDIMVNMLQKFSGVPDNKIVGMAGVLDSARFRTFLADELNVSVQQVQAYVMGGHGDTMVPLTKMSNVAGVSLEQLVKEGKLKQERLDAIVSRTRSGGGEIVALLKTGSAYYAPAAAGIQMAESFLKDKKMILPCAAKVKAGMYGLDEDLFVGVPTEISANGVRPIEVEISDKEREQLQVSINAIKDLNKAAAEILA 318
               SCOP domains d3p7ma1 A:1-145 automated matches                                                                                                                d3p7ma2 A:146-318 automated matches                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eeeehhhhhhhhhhhhhhhhhh.hhh.ee..eee.hhh.eee.....ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeee..hhhhh...eeeeeeeeee..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p7m A   1 mARKKITLVGAGNIGGTLAHLALIKQLGDVVLFDIAQGmPNGKALDLLQTCPIEGVDFKVRGTNDYKDLENSDVVIVTAGVPRKPGmSRDDLLGINIKVmQTVGEGIKHNCPNAFVICITNPLDImVNmLQKFSGVPDNKIVGmAGVLDSARFRTFLADELNVSVQQVQAYVmGGHGDTmVPLTKmSNVAGVSLEQLVKEGKLKQERLDAIVSRTRSGGGEIVALLKTGSAYYAPAAAGIQmAESFLKDKKmILPCAAKVKAGmYGLDEDLFVGVPTEISANGVRPIEVEISDKEREQLQVSINAIKDLNKAAAEILA 318
                            |       10        20        30        40        50        60        70        80      | 90       100       110       120     | 130       140   |   150       160       170  |    180     | 190       200       210       220       230       240 |     250 |     260   |   270       280       290       300       310        
                            |                                    39-MSE                                          87-MSE      100-MSE                   126-MSE           144-MSE                      173-MSE  |     |                                                     242-MSE   252-MSE     264-MSE                                                  
                            1-MSE                                                                                                                         129-MSE                                            180-MSE |                                                                                                                                    
                                                                                                                                                                                                                   186-MSE                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:319
 aligned with Q8G942_FRATL | Q8G942 from UniProtKB/TrEMBL  Length:319

    Alignment length:319
                             1                                                                                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309         
         Q8G942_FRATL     - -MARKKITLVGAGNIGGTLAHLALIKQLGDVVLFDIAQGMPNGKALDLLQTCPIEGVDFKVRGTNDYKDLENSDVVIVTAGVPRKPGMSRDDLLGINIKVMQTVGEGIKHNCPNAFVICITNPLDIMVNMLQKFSGVPDNKIVGMAGVLDSARFRTFLADELNVSVQQVQAYVMGGHGDTMVPLTKMSNVAGVSLEQLVKEGKLKQERLDAIVSRTRSGGGEIVALLKTGSAYYAPAAAGIQMAESFLKDKKMILPCAAKVKAGMYGLDEDLFVGVPTEISANGVRPIEVEISDKEREQLQVSINAIKDLNKAAAEILA 318
               SCOP domains d3p7mb1 B:0-145 automated matches                                                                                                                 d3p7mb2 B:146-318 automated matches                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eeeehhhhhhhhhhhhhhhhhh.hhh.ee..eee.hhh.eee.....ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeee..hhhhh...eeeeeeeeee..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p7m B   0 AmARKKITLVGAGNIGGTLAHLALIKQLGDVVLFDIAQGmPNGKALDLLQTCPIEGVDFKVRGTNDYKDLENSDVVIVTAGVPRKPGmSRDDLLGINIKVmQTVGEGIKHNCPNAFVICITNPLDImVNmLQKFSGVPDNKIVGmAGVLDSARFRTFLADELNVSVQQVQAYVmGGHGDTmVPLTKmSNVAGVSLEQLVKEGKLKQERLDAIVSRTRSGGGEIVALLKTGSAYYAPAAAGIQmAESFLKDKKmILPCAAKVKAGmYGLDEDLFVGVPTEISANGVRPIEVEISDKEREQLQVSINAIKDLNKAAAEILA 318
                             |       9        19        29        39        49        59        69        79       |89        99|      109       119      |129       139    |  149       159       169   |   179|     |189       199       209       219       229       239  |    249  |    259    |  269       279       289       299       309         
                             1-MSE                                39-MSE                                          87-MSE      100-MSE                   126-MSE           144-MSE                      173-MSE  |     |                                                     242-MSE   252-MSE     264-MSE                                                  
                                                                                                                                                           129-MSE                                            180-MSE |                                                                                                                                    
                                                                                                                                                                                                                    186-MSE                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:318
 aligned with Q8G942_FRATL | Q8G942 from UniProtKB/TrEMBL  Length:319

    Alignment length:318
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310        
         Q8G942_FRATL     1 MARKKITLVGAGNIGGTLAHLALIKQLGDVVLFDIAQGMPNGKALDLLQTCPIEGVDFKVRGTNDYKDLENSDVVIVTAGVPRKPGMSRDDLLGINIKVMQTVGEGIKHNCPNAFVICITNPLDIMVNMLQKFSGVPDNKIVGMAGVLDSARFRTFLADELNVSVQQVQAYVMGGHGDTMVPLTKMSNVAGVSLEQLVKEGKLKQERLDAIVSRTRSGGGEIVALLKTGSAYYAPAAAGIQMAESFLKDKKMILPCAAKVKAGMYGLDEDLFVGVPTEISANGVRPIEVEISDKEREQLQVSINAIKDLNKAAAEILA 318
               SCOP domains d3p7mc1 C:1-145 automated matches                                                                                                                d3p7mc2 C:146-318 automated matches                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.hhh.eee.....ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeee..hhhhh...eeeeeeeeee..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p7m C   1 mARKKITLVGAGNIGGTLAHLALIKQLGDVVLFDIAQGmPNGKALDLLQTCPIEGVDFKVRGTNDYKDLENSDVVIVTAGVPRKPGmSRDDLLGINIKVmQTVGEGIKHNCPNAFVICITNPLDImVNmLQKFSGVPDNKIVGmAGVLDSARFRTFLADELNVSVQQVQAYVmGGHGDTmVPLTKmSNVAGVSLEQLVKEGKLKQERLDAIVSRTRSGGGEIVALLKTGSAYYAPAAAGIQmAESFLKDKKmILPCAAKVKAGmYGLDEDLFVGVPTEISANGVRPIEVEISDKEREQLQVSINAIKDLNKAAAEILA 318
                            |       10        20        30        40        50        60        70        80      | 90       100       110       120     | 130       140   |   150       160       170  |    180     | 190       200       210       220       230       240 |     250 |     260   |   270       280       290       300       310        
                            1-MSE                                39-MSE                                          87-MSE      100-MSE                   126-MSE           144-MSE                      173-MSE  |     |                                                     242-MSE   252-MSE     264-MSE                                                  
                                                                                                                                                          129-MSE                                            180-MSE |                                                                                                                                    
                                                                                                                                                                                                                   186-MSE                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:318
 aligned with Q8G942_FRATL | Q8G942 from UniProtKB/TrEMBL  Length:319

    Alignment length:320
                              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
         Q8G942_FRATL     - --MARKKITLVGAGNIGGTLAHLALIKQLGDVVLFDIAQGMPNGKALDLLQTCPIEGVDFKVRGTNDYKDLENSDVVIVTAGVPRKPGMSRDDLLGINIKVMQTVGEGIKHNCPNAFVICITNPLDIMVNMLQKFSGVPDNKIVGMAGVLDSARFRTFLADELNVSVQQVQAYVMGGHGDTMVPLTKMSNVAGVSLEQLVKEGKLKQERLDAIVSRTRSGGGEIVALLKTGSAYYAPAAAGIQMAESFLKDKKMILPCAAKVKAGMYGLDEDLFVGVPTEISANGVRPIEVEISDKEREQLQVSINAIKDLNKAAAEILA 318
               SCOP domains d3p7md1 D:-1-145 automated matches                                                                                                                 d3p7md2 D:146-318 automated matches                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee......--..hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.hhh.eee.....ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeee..hhhhh...eeeeeeeeee..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p7m D  -1 NAmARKKITLVGAGNIGGTLAHLALIKQLGDVVLFDIAQGmPNGKALDLLQTCPIEGVDFKVRGTNDYKDLENSDVVIVTAGVPR--GmSRDDLLGINIKVmQTVGEGIKHNCPNAFVICITNPLDImVNmLQKFSGVPDNKIVGmAGVLDSARFRTFLADELNVSVQQVQAYVmGGHGDTmVPLTKmSNVAGVSLEQLVKEGKLKQERLDAIVSRTRSGGGEIVALLKTGSAYYAPAAAGIQmAESFLKDKKmILPCAAKVKAGmYGLDEDLFVGVPTEISANGVRPIEVEISDKEREQLQVSINAIKDLNKAAAEILA 318
                              |      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
                              1-MSE                                39-MSE                                      83 86|          100-MSE                   126-MSE           144-MSE                      173-MSE  |     |                                                     242-MSE   252-MSE     264-MSE                                                  
                                                                                                                   87-MSE                                   129-MSE                                            180-MSE |                                                                                                                                    
                                                                                                                                                                                                                     186-MSE
   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  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P7M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3P7M)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q8G942_FRATL | Q8G942)
molecular function
    GO:0030060    L-malate dehydrogenase activity    Catalysis of the reaction: (S)-malate + NAD+ = oxaloacetate + NADH + H+.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0019752    carboxylic acid metabolic process    The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
    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:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.

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  3p7m
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 Related Entries

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