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(-) Description

Title :  CRYSTAL STRUCTURE OF NADPH-DEPENDENT GLYOXYLATE/HYDROXYPYRUVATE REDUCTASE SMC04462 (SMGHRB) FROM SINORHIZOBIUM MELILOTI IN COMPLEX WITH CITRATE
 
Authors :  I. G. Shabalin, K. B. Handing, O. A. Gasiorowska, D. R. Cooper, D. Matels J. Bonanno, S. C. Almo, W. Minor, New York Structural Genomics Res Consortium (Nysgrc)
Date :  17 Mar 17  (Deposition) - 29 Mar 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase, Nadp, Nysgrc, Sinorhizobium Meliloti, Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. G. Shabalin, K. B. Handing, W. Minor
Evolutionary, Biochemical, And Structural Studies On D-2-Hydroxyacid Dehydrogenases From Sinorhizium Meliloti 1021 Indicate A Subdivision Of The Glyoxylate/Hydroxypyruvate Reductases
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NADPH-DEPENDENT GLYOXYLATE/HYDROXYPYRUVATE REDUCTASE
    Chains: A, B, C, D
    EC Number: 1.1.1.81, 1.1.1.79
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSGC-HIS
    Expression System Strain: BL21 (DE3)-RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SMC04462
    Organism Common: ENSIFER MELILOTI
    Organism Scientific: RHIZOBIUM MELILOTI (STRAIN 1021)
    Organism Taxid: 266834
    Other Details: HIS-TAG-LABELLED PROTEIN WAS SUBJECTED TO LIMITED PROTEOLYSIS BY CHYMOTRYPSIN IMMEDIATELY PRIOR TO CRYSTALLIZATION.
    Strain: 1021

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CL4Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4NA5Ligand/IonSODIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CIT-1Ligand/IonCITRIC ACID
2CL-1Ligand/IonCHLORIDE ION
3GOL-1Ligand/IonGLYCEROL
4NA-1Ligand/IonSODIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:191 , GLU A:192 , VAL A:194 , ALA A:218 , LEU A:219 , HOH A:668binding site for residue NA A 401
02AC2SOFTWAREASN A:13 , ARG A:286 , HOH A:774 , HOH A:776binding site for residue CL A 402
03AC3SOFTWARELEU A:96 , GLY A:229 , HIS A:277 , SER A:280binding site for residue GOL A 403
04AC4SOFTWAREALA B:191 , GLU B:192 , VAL B:194 , ALA B:218 , LEU B:219 , HOH C:667binding site for residue NA B 401
05AC5SOFTWAREASN B:13 , ARG B:286 , HOH B:699binding site for residue CL B 402
06AC6SOFTWAREALA C:191 , GLU C:192 , VAL C:194 , ALA C:218 , LEU C:219 , HOH C:615 , HOH C:715binding site for residue NA C 401
07AC7SOFTWAREVAL C:228 , GLY C:229 , CIT C:403 , HOH C:638binding site for residue NA C 402
08AC8SOFTWAREVAL C:72 , ILE C:153 , VAL C:228 , GLY C:229 , HIS C:277 , ALA C:279 , SER C:280 , NA C:402 , HOH C:501 , HOH C:529 , HOH C:562 , HOH C:582 , HOH C:584 , HOH C:634 , HOH C:638binding site for residue CIT C 403
09AC9SOFTWAREASN C:13 , ARG C:286 , HOH C:776binding site for residue CL C 404
10AD1SOFTWAREALA D:191 , GLU D:192 , VAL D:194 , ALA D:218 , LEU D:219 , HOH D:647binding site for residue NA D 401
11AD2SOFTWAREASN D:13 , ARG D:286 , HOH D:679binding site for residue CL D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5V72)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:259 -Pro A:260
2Glu B:259 -Pro B:260
3Glu C:259 -Pro C:260
4Glu D:259 -Pro D:260

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5V72)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V72)

(-) Exons   (0, 0)

(no "Exon" information available for 5V72)

(-) 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:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhh.eeeee...hhhhhhhhhhhh.eeee....hhhhhh......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeee.hhhhhhhhhhhhhhh..eeeee..........eee.hhhhhhhhh.eeee.........hhhhhhhhh...eeee.......hhhhhhhhhhh....eeee.........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5v72 A   1 MSRPRILVPGKINPRVLERLPEMFETVRIERADAALVTADMRDVSGIAVSGKLPVPLMDAFPSLEIVANFGVGYDGVDVSRAAARGIVVTNTPDVLTEEVADTAIGLLLNTLRLLPQAEQWLRQGRWVREGAFPLSPLSLRGRTVGLFGLGRIGLAIARRLEAFGVSIAYHTRTPREGLGFTYHPTLVGMAEAVDTLIVIVPGTLKAVNADVLSALGPKGVLINVGRGSTVDEAALVTALQNGTIAGAGLDVFENEPNVPEALLSFPNVSLLPHVASASVVTRNAMSDLVVDNLKAWFSTGEALTPVAETPFRRRAIQ 321
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  ||   213       223       233       243       253       263       273       283       293       303       313        
                                                                                                                                                                                                                                    203|                                                                                                                  
                                                                                                                                                                                                                                     207                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhh.eeeee...hhhhhhhhhhhh.eeee....hhhhhh......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee.hhhhhhhhhhhhhhh..eeeee..........ee..hhhhhhhhh.eeee..........hhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v72 B   3 RPRILVPGKINPRVLERLPEMFETVRIERADAALVTADMRDVSGIAVSGKLPVPLMDAFPSLEIVANFGVGYDGVDVSRAAARGIVVTNTPDVLTEEVADTAIGLLLNTLRLLPQAEQWLRQGRWVREGAFPLSPLSLRGRTVGLFGLGRIGLAIARRLEAFGVSIAYHTRTPREGLGFTYHPTLVGMAEAVDTLIVIVPASTLKAVNADVLSALGPKGVLINVGRGSTVDEAALVTALQNGTIAGAGLDVFENEPNVPEALLSFPNVSLLPHVASASVVTRNAMSDLVVDNLKAWFSTGEALTPVAETPFRR 317
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202|      214       224       234       244       254       264       274       284       294       304       314   
                                                                                                                                                                                                                                 202|                                                                                                                
                                                                                                                                                                                                                                  205                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:320
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhh.eeeee...hhhhhhhhhhhh.eeee....hhhhhh......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeee.hhhhhhhhhhhhhhh..eeeee..........eee.hhhhhhhhh.eeee............hhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v72 C   3 RPRILVPGKINPRVLERLPEMFETVRIERADAALVTADMRDVSGIAVSGKLPVPLMDAFPSLEIVANFGVGYDGVDVSRAAARGIVVTNTPDVLTEEVADTAIGLLLNTLRLLPQAEQWLRQGRWVREGAFPLSPLSLRGRTVGLFGLGRIGLAIARRLEAFGVSIAYHTRTPREGLGFTYHPTLVGMAEAVDTLIVIVPGTASTLKAVNADVLSALGPKGVLINVGRGSTVDEAALVTALQNGTIAGAGLDVFENEPNVPEALLSFPNVSLLPHVASASVVTRNAMSDLVVDNLKAWFSTGEALTPVAETPFRRRAIQN 322
                                    12        22        32        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


Chain D from PDB  Type:PROTEIN  Length:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhh.eeeee...hhhhhhhhhhhh.eeee....hhhhhh......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeee.hhhhhhhhhhhhhhh..eeeee..........eee.hhhhhhhhh.eeee........hhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v72 D   3 RPRILVPGKINPRVLERLPEMFETVRIERADAALVTADMRDVSGIAVSGKLPVPLMDAFPSLEIVANFGVGYDGVDVSRAAARGIVVTNTPDVLTEEVADTAIGLLLNTLRLLPQAEQWLRQGRWVREGAFPLSPLSLRGRTVGLFGLGRIGLAIARRLEAFGVSIAYHTRTPREGLGFTYHPTLVGMAEAVDTLIVIVSTLKAVNADVLSALGPKGVLINVGRGSTVDEAALVTALQNGTIAGAGLDVFENEPNVPEALLSFPNVSLLPHVASASVVTRNAMSDLVVDNLKAWFSTGEALTPVAETPFRRRA 319
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       206       216       226       236       246       256       266       276       286       296       306       316   
                                                                                                                                                                                                                                201|                                                                                                                 
                                                                                                                                                                                                                                 206
   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 5V72)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V72)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V72)

(-) Gene Ontology  (4, 4)

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  5v72
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  Q92LZ4_RHIME | Q92LZ4
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 Related Entries

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

UniProtKB/TrEMBL
        Q92LZ4_RHIME | Q92LZ4: 5j23 5uog 5v6q 5v7g 5v7n

(-) Related Entries Specified in the PDB File

5j23 SMGHRB, COMPLEX WITH 2'-PHOSPHO-ADP-RIBOSE RELATED ID: NYSGRC-012132 RELATED DB: TARGETTRACK RELATED ID: 012132 RELATED DB: TARGETTRACK
5uog SMGHRB, APO FORM
5v6q SMGHRB, COMPLEX WITH NADP AND MALONATE