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(-) Description

Title :  STRUCTURAL BASIS FOR LIGHT ACITVATION OF A CHLOROPLAST ENZYME. THE STRUCTURE OF SORGHUM NADP-MALATE DEHYDROGENASE IN ITS OXIDIZED FORM
 
Authors :  K. Johansson, S. Ramaswamy, M. Saarinen, M. Lemaire-Chamley, E. Issak Bourguet, M. Miginiac-Maslow, H. Eklund
Date :  16 Feb 99  (Deposition) - 04 Jun 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B  (2x)
Biol. Unit 4:  C,D  (2x)
Keywords :  Chloroplastic Malate Dehydrogenase (Nadp+), Activated By Light, Chloroplastic Malate Dehydrogenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Johansson, S. Ramaswamy, M. Saarinen, M. Lemaire-Chamley, E. Issakidis-Bourguet, M. Miginiac-Maslow, H. Eklund
Structural Basis For Light Activation Of A Chloroplast Enzyme: The Structure Of Sorghum Nadp-Malate Dehydrogenase In Its Oxidized Form.
Biochemistry V. 38 4319 1999
PubMed-ID: 10194350  |  Reference-DOI: 10.1021/BI982876C

(-) Compounds

Molecule 1 - PROTEIN (MALATE DEHYDROGENASE)
    Chains: A, B, C, D
    EC Number: 1.1.1.82
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organelle: CHLOROPLAST
    Organism Common: SORGHUM
    Organism Scientific: SORGHUM BICOLOR
    Organism Taxid: 4558
    Tissue: LEAF

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (2x): AB  
Biological Unit 4 (2x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 17)

Asymmetric Unit (1, 17)
No.NameCountTypeFull Name
1ZN17Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:173 , CYS A:175 , LEU A:197 , HIS A:229 , HOH A:525BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWAREGLU A:320 , ASP A:321 , LYS A:363 , GLU A:372BINDING SITE FOR RESIDUE ZN A 502
03AC3SOFTWAREASP A:201 , HIS A:229 , LEU A:385 , HOH A:524BINDING SITE FOR RESIDUE ZN A 503
04AC4SOFTWAREASP A:23 , GLU A:118 , GLU A:121 , GLU D:86BINDING SITE FOR RESIDUE ZN A 504
05AC5SOFTWAREGLU B:109 , HOH B:512 , ASP D:346 , GLU D:350BINDING SITE FOR RESIDUE ZN B 501
06AC6SOFTWAREASP B:122 , HOH B:516 , HOH B:517 , THR D:254 , GLU D:258BINDING SITE FOR RESIDUE ZN B 502
07AC7SOFTWAREASP B:201 , HIS B:229 , LEU B:385 , HOH B:543BINDING SITE FOR RESIDUE ZN B 503
08AC8SOFTWAREASN B:173 , CYS B:175 , HIS B:229BINDING SITE FOR RESIDUE ZN B 504
09AC9SOFTWARETHR B:254 , GLU B:258 , ASP D:122BINDING SITE FOR RESIDUE ZN B 505
10BC1SOFTWAREHIS B:368 , HOH B:558 , GLU C:93 , LYS D:275 , HOH D:586BINDING SITE FOR RESIDUE ZN C 501
11BC2SOFTWAREGLU C:320 , ASP C:321 , LYS C:363 , GLU C:372BINDING SITE FOR RESIDUE ZN C 502
12BC3SOFTWAREASP C:201 , HIS C:229BINDING SITE FOR RESIDUE ZN C 503
13BC4SOFTWAREASN C:173 , CYS C:175 , HIS C:229 , HOH C:523BINDING SITE FOR RESIDUE ZN C 504
14BC5SOFTWAREGLU A:93 , ASP D:145 , HIS D:368BINDING SITE FOR RESIDUE ZN D 501
15BC6SOFTWAREASP D:201 , HIS D:229BINDING SITE FOR RESIDUE ZN D 502
16BC7SOFTWAREASP B:346 , GLU B:350 , GLU D:109 , HOH D:568BINDING SITE FOR RESIDUE ZN D 503
17BC8SOFTWARELYS C:275 , GLU D:93BINDING SITE FOR RESIDUE ZN C 505
18CAAAUTHORASP A:201 , HIS A:229NULL
19CABAUTHORASP B:201 , HIS B:229NULL
20CACAUTHORASP C:201 , HIS C:229NULL
21CADAUTHORASP D:201 , HIS D:229NULL
22CSAAUTHORCYS A:365 , CYS A:377NULL
23CSBAUTHORCYS B:365 , CYS B:377NULL
24CSCAUTHORCYS C:365 , CYS C:377NULL
25CSDAUTHORCYS D:365 , CYS D:377NULL
26NSAAUTHORCYS A:24 , CYS A:29NULL
27NSBAUTHORCYS B:24 , CYS B:29N-TERMINAL REDOX-REGULATED DISULFIDE
28NSCAUTHORCYS C:24 , CYS C:29NULL
29NSDAUTHORCYS D:24 , CYS D:29NULL

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:24 -A:29
2A:365 -A:377
3B:24 -B:29
4B:365 -B:377
5C:24 -C:29
6C:365 -C:377
7D:24 -D:29
8D:365 -D:377

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:173 -Pro A:174
2Asn B:173 -Pro B:174
3Asn C:173 -Pro C:174
4Asn D:173 -Pro D:174

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 7MDH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 7MDH)

(-) Exons   (0, 0)

(no "Exon" information available for 7MDH)

(-) 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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d7mdha1 A:23-197 Malate dehydrogenase                                                                                                                              d7mdha2 A:198-385 Malate dehydrogenase                                                                                                                                                       SCOP domains
               CATH domains ---------7mdhA01 A:44-196 NAD(P)-binding Rossmann-like Domain                                                                                                     7mdhA02 A:197-369 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                  ---------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh......eeeeee....hhhhhhhhhhhh.........eeeeee..hhhhhhhhhhhhhhhhh....eeeeeee..hhhh.....eeee...........hhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhh.....hhheee..hhhhhhhhhhhhhh....hhh....eee.......eee..........hhh....hhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhh........eeeeee............eeeeee.................hhhhhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 7mdh A  23 DCFGVFCTWKKLVNIAVSGAAGMISNHLLFKLASGEVFGQDQPIALKLLGSERSFQALEGVAMELEDSLYPLLREVSIGIDPYEVFEDVDWALLIGAKPRGPGMERAALLDINGQIFADQGKALNAVASKNVKVLVVGNPCNTNALICLKNAPDIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNVTIWGNHSTTQVPDFLNAKIDGRPVKEVIKRTKWLEEEFTITVQKRGGALIQKWGRSSAASTAVSIADAIKSLVTPTPEGDWFSTGVYTTGNPYGIAEDIVFSMPCRSKGDGDYELATDVSNDDFLWERIKKSEAELLAEKKCVAHLTGEGNAYCDVPEDTML 385
                                   |44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384 
                                  30|                                                                                                                                                                                                                                                                                                                                                      
                                   43                                                                                                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d7mdhb1 B:21-197 Malate dehydrogenase                                                                                                                                      d7mdhb2 B:198-386 Malate dehydrogenase                                                                                                                                                        SCOP domains
               CATH domains -----------------7mdhB01 B:44-196 NAD(P)-binding Rossmann-like Domain                                                                                                     7mdhB02 B:197-369 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                  ----------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhh..........eeeeee....hhhhhhhhhhh..........eeeeee.....hhhhhhhhhhhhhh....eeeeeee..hhhh.....eeee...........hhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhh.....hhheee..hhhhhhhhhhhhhh....hhh....eee.......eee..........hhhh...hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh........eeeeee............eeeeee.................hhhhhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 7mdh B  21 RKDCFGVFCTTYDLKSWKKLVNIAVSGAAGMISNHLLFKLASGEVFGQDQPIALKLLGSERSFQALEGVAMELEDSLYPLLREVSIGIDPYEVFEDVDWALLIGAKPRGPGMERAALLDINGQIFADQGKALNAVASKNVKVLVVGNPCNTNALICLKNAPDIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNVTIWGNHSTTQVPDFLNAKIDGRPVKEVIKRTKWLEEEFTITVQKRGGALIQKWGRSSAASTAVSIADAIKSLVTPTPEGDWFSTGVYTTGNPYGIAEDIVFSMPCRSKGDGDYELATDVSNDDFLWERIKKSEAELLAEKKCVAHLTGEGNAYCDVPEDTMLP 386
                                    30    ||  46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386
                                         35|                                                                                                                                                                                                                                                                                                                                                        
                                          42                                                                                                                                                                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d7mdhc1 C:23-197 Malate dehydrogenase                                                                                                                                d7mdhc2 C:198-384 Malate dehydrogenase                                                                                                                                                      SCOP domains
               CATH domains -----------7mdhC01 C:44-196 NAD(P)-binding Rossmann-like Domain                                                                                                     7mdhC02 C:197-369 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                  --------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.......eeeeee....hhhhhhhhhhhh.........eeeeee.....hhhhhhhhhhhhhh....eeeeeee..hhhh.....eeee...........hhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhh.....hhheee..hhhhhhhhhhhhhh....hhh....eee.......eee..........hhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh........eeeeee............eeeeee.................hhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 7mdh C  23 DCFGVFCTTSWKKLVNIAVSGAAGMISNHLLFKLASGEVFGQDQPIALKLLGSERSFQALEGVAMELEDSLYPLLREVSIGIDPYEVFEDVDWALLIGAKPRGPGMERAALLDINGQIFADQGKALNAVASKNVKVLVVGNPCNTNALICLKNAPDIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNVTIWGNHSTTQVPDFLNAKIDGRPVKEVIKRTKWLEEEFTITVQKRGGALIQKWGRSSAASTAVSIADAIKSLVTPTPEGDWFSTGVYTTGNPYGIAEDIVFSMPCRSKGDGDYELATDVSNDDFLWERIKKSEAELLAEKKCVAHLTGEGNAYCDVPEDTM 384
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382  
                                   31|                                                                                                                                                                                                                                                                                                                                                      
                                    42                                                                                                                                                                                                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d7mdhd1 D:21-197 Malate dehydrogenase                                                                                                                                   d7mdhd2 D:198-381 Malate dehydrogenase                                                                                                                                                   SCOP domains
               CATH domains --------------7mdhD01 D:44-196 NAD(P)-binding Rossmann-like Domain                                                                                                     7mdhD02 D:197-369 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                  ------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.......eeeeee....hhhhhhhhhhhh.........eeeeee..hhhhhhhhhhhhhhhhh....eeeeeee..hhhh.....eeee...........hhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhh......hhheee..hhhhhhhhhhhhhh....hhh....eee.......eee..........hhhh...hhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.........eeeeee............eeeeee.................hhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 7mdh D  21 RKDCFGVFCTTYDWKKLVNIAVSGAAGMISNHLLFKLASGEVFGQDQPIALKLLGSERSFQALEGVAMELEDSLYPLLREVSIGIDPYEVFEDVDWALLIGAKPRGPGMERAALLDINGQIFADQGKALNAVASKNVKVLVVGNPCNTNALICLKNAPDIPAKNFHALTRLDENRAKCQLALKAGVFYDKVSNVTIWGNHSTTQVPDFLNAKIDGRPVKEVIKRTKWLEEEFTITVQKRGGALIQKWGRSSAASTAVSIADAIKSLVTPTPEGDWFSTGVYTTGNPYGIAEDIVFSMPCRSKGDGDYELATDVSNDDFLWERIKKSEAELLAEKKCVAHLTGEGNAYCDVPE 381
                                    30  ||    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       319       329       339       349       359       369       379  
                                       33|                                                                                                                                                                                                                                                                                                                                                  
                                        43
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  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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 7MDH)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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  7mdh
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