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(-) Description

Title :  1.7 A RESOLUTION STRUCTURE OF WILD TYPE MALATE DEHYDROGENASE FROM HALOARCULA MARISMORTUI
 
Authors :  F. M. D. Vellieux
Date :  22 Feb 13  (Deposition) - 20 Mar 13  (Release) - 20 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Halophile, Oxidoreductase, Malate Dehydrogenase Tricarboxylic Acid Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. M. D. Vellieux
1. 7 A Resolution Structure Of Wild Type Malate Dehydrogenas From Haloarcula Marismortui
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) 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: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MDH, RRNAC2706
    Organism Scientific: HALOARCULA MARISMORTUI
    Organism Taxid: 2238
    Strain: HMS174

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 39)

Asymmetric/Biological Unit (2, 39)
No.NameCountTypeFull Name
1CL13Ligand/IonCHLORIDE ION
2NA26Ligand/IonSODIUM ION

(-) Sites  (39, 39)

Asymmetric Unit (39, 39)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:205 , ASP A:306 , THR D:210A , ASP D:211BINDING SITE FOR RESIDUE CL A 401
02AC2SOFTWAREARG A:166 , HIS A:256 , TYR B:72 , ASP B:73 , HOH B:537BINDING SITE FOR RESIDUE CL A 402
03AC3SOFTWAREGLY A:69 , ILE A:70 , ALA A:71 , TYR A:72 , ASP A:73 , ARG B:166 , ARG B:252BINDING SITE FOR RESIDUE CL A 403
04AC4SOFTWAREHIS A:68 , GLY A:69 , ARG B:166 , GLY B:249BINDING SITE FOR RESIDUE CL A 404
05AC5SOFTWAREASP A:47 , ASP C:264 , HOH C:818BINDING SITE FOR RESIDUE NA A 405
06AC6SOFTWARESER A:91 , ASN A:131 , ASP A:132B , HOH A:577BINDING SITE FOR RESIDUE NA A 406
07AC7SOFTWARETYR A:150 , GLU A:151 , GLY A:153 , HOH A:592 , HOH A:594BINDING SITE FOR RESIDUE NA A 407
08AC8SOFTWAREGLU A:247 , GLU B:247 , HOH B:556 , HOH B:773BINDING SITE FOR RESIDUE NA A 408
09AC9SOFTWAREASP A:264 , HOH A:715 , ASP C:47 , HOH C:517BINDING SITE FOR RESIDUE NA A 409
10BC1SOFTWAREASN A:67 , THR A:76 , HOH A:530 , TYR B:174 , HOH B:591BINDING SITE FOR RESIDUE NA A 410
11BC2SOFTWARELYS B:205 , ASP B:306 , THR C:210A , ASP C:211BINDING SITE FOR RESIDUE CL B 401
12BC3SOFTWAREARG B:171 , HOH B:542 , HOH B:602BINDING SITE FOR RESIDUE CL B 402
13BC4SOFTWAREVAL A:184 , HOH A:754 , ILE B:70 , SER B:74 , ASN B:75 , THR B:76 , HOH B:701BINDING SITE FOR RESIDUE NA B 403
14BC5SOFTWARESER B:91 , ASP B:132B , HOH B:783 , HOH B:785 , HOH B:832BINDING SITE FOR RESIDUE NA B 404
15BC6SOFTWAREGLY B:196 , GLN B:199 , HOH B:604 , HOH B:724 , HOH B:805 , HOH B:858BINDING SITE FOR RESIDUE NA B 405
16BC7SOFTWAREASP B:264 , HOH B:642 , ASP D:47 , HOH D:787BINDING SITE FOR RESIDUE NA B 406
17BC8SOFTWAREGLU B:151 , GLY B:153 , HOH B:800 , HOH B:821 , HOH B:854BINDING SITE FOR RESIDUE NA B 407
18BC9SOFTWAREGLY C:69 , ILE C:70 , ALA C:71 , TYR C:72 , ASP C:73 , ARG D:166 , ARG D:252BINDING SITE FOR RESIDUE CL C 401
19CC1SOFTWARETHR B:210A , ASP B:211 , LYS C:205 , ASP C:306BINDING SITE FOR RESIDUE CL C 402
20CC2SOFTWAREARG C:166 , ARG C:252 , HIS C:256 , TYR D:72 , ASP D:73 , HOH D:544BINDING SITE FOR RESIDUE CL C 403
21CC3SOFTWAREARG C:171 , THR C:246BINDING SITE FOR RESIDUE CL C 404
22CC4SOFTWAREASP C:111 , ASP C:115 , HOH C:530 , HOH C:892BINDING SITE FOR RESIDUE NA C 405
23CC5SOFTWARETYR C:150 , GLU C:151 , GLY C:153 , NA C:407 , HOH C:587 , HOH C:589BINDING SITE FOR RESIDUE NA C 406
24CC6SOFTWAREGLU C:151 , GLY C:153 , NA C:406 , NA C:410 , HOH C:698 , HOH C:751BINDING SITE FOR RESIDUE NA C 407
25CC7SOFTWARESER C:177 , GLU C:178 , HOH C:599 , HOH C:604BINDING SITE FOR RESIDUE NA C 408
26CC8SOFTWAREASP C:211 , PRO C:212 , GLU C:219 , HOH C:552 , HOH C:622BINDING SITE FOR RESIDUE NA C 409
27CC9SOFTWAREGLY C:153 , ASP C:154 , NA C:407 , HOH C:752 , HOH C:763BINDING SITE FOR RESIDUE NA C 410
28DC1SOFTWARETHR A:210A , ASP A:211 , HOH A:548 , LYS D:205 , ASP D:306BINDING SITE FOR RESIDUE CL D 401
29DC2SOFTWAREARG D:171 , THR D:246 , HOH D:502 , HOH D:649BINDING SITE FOR RESIDUE CL D 402
30DC3SOFTWAREARG C:166 , ARG C:252 , GLY D:69 , ILE D:70 , ALA D:71 , TYR D:72 , ASP D:73BINDING SITE FOR RESIDUE CL D 403
31DC4SOFTWARETHR D:22 , ILE D:45 , HOH D:520 , HOH D:708BINDING SITE FOR RESIDUE NA D 404
32DC5SOFTWAREHOH C:599 , ASN D:67 , THR D:76 , HOH D:540BINDING SITE FOR RESIDUE NA D 405
33DC6SOFTWARESER D:91 , ASP D:132B , HOH D:553 , HOH D:554BINDING SITE FOR RESIDUE NA D 406
34DC7SOFTWARETYR D:150 , GLU D:151 , GLY D:153 , NA D:408 , HOH D:597 , HOH D:806BINDING SITE FOR RESIDUE NA D 407
35DC8SOFTWAREGLU D:151 , GLY D:153 , NA D:407 , HOH D:752 , HOH D:807BINDING SITE FOR RESIDUE NA D 408
36DC9SOFTWARESER D:204 , VAL D:206 , ASP D:211 , PRO D:212 , HOH D:621 , HOH D:629BINDING SITE FOR RESIDUE NA D 409
37EC1SOFTWAREHOH C:649 , HOH C:817 , THR D:31 , ALA D:35 , GLU D:247BINDING SITE FOR RESIDUE NA D 410
38EC2SOFTWAREHOH C:733 , SER D:177 , GLU D:178 , HOH D:722BINDING SITE FOR RESIDUE NA D 411
39EC3SOFTWAREGLY D:28 , GLY D:30 , ASP D:53 , HOH D:527 , HOH D:533 , HOH D:558 , HOH D:731BINDING SITE FOR RESIDUE NA D 412

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JCO)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:140 -Pro A:141
2Asn B:140 -Pro B:141
3Asn C:140 -Pro C:141
4Asn D:140 -Pro D:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JCO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JCO)

(-) Exons   (0, 0)

(no "Exon" information available for 4JCO)

(-) 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:303
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4jcoa1 A:22-162 automated matches                                                                                                            d4jcoa2 A:163-330 automated matches                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh..hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.....eee.hhhhee.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jco A   22 TKVSVVGAAGTVGAAAGYNIALRDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVRQGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVPVFSKVRVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTGEVLPASVKLEGEFGHEDTAFGVPVRLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDKIS  330
                                   |30        40        50    ||  58        68        78  ||    90       100  ||   111       121       131||     140       150       160       170       180       190       200       210| ||   225       235       245       255       265       275    || 286       296  ||   307       317       327   
                                 29A|                       54A|                         81|                103|                       132A|                                                                           210A ||                                                          280|              299|                             
                                  29B                        54B                          84                 105                        132B                                                                              212|                                                           282               301                             
                                                                                                                                                                                                                           219                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4jcob1 B:22-162 automated matches                                                                                                            d4jcob2 B:163-330 automated matches                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh..hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.....eee.hhhhee.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jco B   22 TKVSVVGAAGTVGAAAGYNIALRDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVRQGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVPVFSKVRVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTGEVLPASVKLEGEFGHEDTAFGVPVRLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDKIS  330
                                   |30        40        50    ||  58        68        78  ||    90       100  ||   111       121       131||     140       150       160       170       180       190       200       210| ||   225       235       245       255       265       275    || 286       296  ||   307       317       327   
                                 29A|                       54A|                         81|                103|                       132A|                                                                           210A ||                                                          280|              299|                             
                                  29B                        54B                          84                 105                        132B                                                                              212|                                                           282               301                             
                                                                                                                                                                                                                           219                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4jcoc1 C:22-162 automated matches                                                                                                            d4jcoc2 C:163-330 automated matches                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh..hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.....eee.hhhhee.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jco C   22 TKVSVVGAAGTVGAAAGYNIALRDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVRQGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVPVFSKVRVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTGEVLPASVKLEGEFGHEDTAFGVPVRLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDKIS  330
                                   |30        40        50    ||  58        68        78  ||    90       100  ||   111       121       131||     140       150       160       170       180       190       200       210| ||   225       235       245       255       265       275    || 286       296  ||   307       317       327   
                                 29A|                       54A|                         81|                103|                       132A|                                                                           210A ||                                                          280|              299|                             
                                  29B                        54B                          84                 105                        132B                                                                              212|                                                           282               301                             
                                                                                                                                                                                                                           219                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4jcod1 D:22-162 automated matches                                                                                                            d4jcod2 D:163-330 automated matches                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh..hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.....eee.hhhhee.......hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jco D   22 TKVSVVGAAGTVGAAAGYNIALRDIADEVVFVDIPDKEDDTVGQAADTNHGIAYDSNTRVRQGGYEDTAGSDVVVITAGIPRQPGQTRIDLAGDNAPIMEDIQSSLDEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGGRLDSARFRYVLSEEFDAPVQNVEGTILGEHGDAQVPVFSKVRVDGTDPEFSGDEKEQLLGDLQESAMDVIERKGATEWGPARGVAHMVEAILHDTGEVLPASVKLEGEFGHEDTAFGVPVRLGSNGVEEIVEWDLDDYEQDLMADAAEKLSDQYDKIS  330
                                   |30        40        50    ||  58        68        78  ||    90       100  ||   111       121       131||     140       150       160       170       180       190       200       210| ||   225       235       245       255       265       275    || 286       296  ||   307       317       327   
                                 29A|                       54A|                         81|                103|                       132A|                                                                           210A ||                                                          280|              299|                             
                                  29B                        54B                          84                 105                        132B                                                                              212|                                                           282               301                             
                                                                                                                                                                                                                           219
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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, 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 4JCO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JCO)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MDH_HALMA | Q07841: 1d3a 1hlp 1o6z 2hlp 2j5k 2j5q 2j5r 2x0r

(-) Related Entries Specified in the PDB File

1d3a CRYSTAL STRUCTURE OF THE WILD TYPE HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM
1gt2 R207S,R292S MUTANT OF MALATE DEHYDROGENASE FROM THE HALOPHILIC ARCHAEON HALOARCULA MARISMORTUI (HOLO FORM)
1hlp MALATE DEHYDROGENASE (HALOPHILIC) COMPLEXED WITH NICOTINAMIDE ADENINE DINUCLEOTIDE (NAD)
1o6z 1.95 A RESOLUTION STRUCTURE OF (R207S, R292S) MUTANT OF MALATE DEHYDROGENASE FROM THE HALOPHILIC ARCHAEON HALOARCULA MARISMORTUI (HOLO FORM)
2hlp CRYSTAL STRUCTURE OF THE E267R MUTANT OF A HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM
2j5k 2.0 A RESOLUTION STRUCTURE OF THE WILD TYPE MALATE DEHYDROGENASE FROM HALOARCULA MARISMORTUI (RADIATION DAMAGE SERIES)
2j5q 2.15 A RESOLUTION STRUCTURE OF THE WILD TYPE MALATE DEHYDROGENASE FROM HALOARCULA MARISMORTUI AFTER FIRST RADIATION BURN (RADIATION DAMAGE SERIES)
2j5r 2.25 A RESOLUTION STRUCTURE OF THE WILD TYPE MALATE DEHYDROGENASE FROM HALOARCULA MARISMORTUI AFTER SECOND RADIATION BURN (RADIATION DAMAGE SERIES)