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(-) Description

Title :  CRYSTAL STRUCTURE OF NADPH-DEPENDENT GLYOXYLATE/HYDROXYPYRUVATE REDUCTASE SMC04462 (SMGHRB) FROM SINORHIZOBIUM MELILOTI IN COMPLEX WITH NADPH AND OXALATE
 
Authors :  I. G. Shabalin, D. V. Mason, K. B. Handing, J. Kutner, D. Matelska, D. R. C J. Bonanno, S. C. Almo, W. Minor, New York Structural Genomics Res Consortium (Nysgrc)
Date :  20 Mar 17  (Deposition) - 29 Mar 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,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) RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SMC04462
    Organism Common: ENSIFER MELILOTI
    Organism Scientific: RHIZOBIUM MELILOTI (STRAIN 1021)
    Organism Taxid: 266834
    Strain: 1021
    Synonym: 2-HYDROXYACID DEHYDROGENASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric Unit (5, 19)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3NA4Ligand/IonSODIUM ION
4NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
5OXL4Ligand/IonOXALATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
5OXL2Ligand/IonOXALATE ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
5OXL2Ligand/IonOXALATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:71 , VAL A:72 , GLY A:73 , LEU A:96 , ARG A:230 , HIS A:277 , NDP A:402 , HOH A:504 , HOH A:671binding site for residue OXL A 401
02AC2SOFTWAREVAL A:72 , VAL A:100 , PHE A:148 , LEU A:150 , GLY A:151 , ARG A:152 , ILE A:153 , THR A:172 , ARG A:173 , THR A:174 , ILE A:200 , VAL A:201 , PRO A:202 , SER A:206 , THR A:207 , VAL A:228 , GLY A:229 , ARG A:230 , ASP A:254 , VAL A:255 , HIS A:277 , ALA A:279 , OXL A:401 , HOH A:503 , HOH A:504 , HOH A:511 , HOH A:536 , HOH A:545 , HOH A:556 , HOH A:590 , HOH A:617 , HOH A:626 , HOH A:636 , HOH A:639 , HOH A:641 , HOH A:644 , HOH A:704 , HOH A:733binding site for residue NDP A 402
03AC3SOFTWAREVAL A:95 , THR A:285 , HOH A:569 , HOH A:580 , HOH A:620 , HOH A:650 , ARG B:141binding site for residue GOL A 403
04AC4SOFTWAREASN A:13 , ARG A:286 , HOH A:777binding site for residue CL A 404
05AC5SOFTWAREALA A:191 , GLU A:192 , VAL A:194 , ALA A:218 , LEU A:219 , HOH A:754binding site for residue NA A 405
06AC6SOFTWAREGLY B:71 , VAL B:72 , GLY B:73 , LEU B:96 , ARG B:230 , HIS B:277 , NDP B:402 , HOH B:501 , HOH B:527 , HOH B:557binding site for residue OXL B 401
07AC7SOFTWAREVAL B:72 , GLY B:73 , VAL B:100 , PHE B:148 , LEU B:150 , GLY B:151 , ARG B:152 , ILE B:153 , THR B:172 , ARG B:173 , THR B:174 , ILE B:200 , VAL B:201 , PRO B:202 , SER B:206 , THR B:207 , VAL B:228 , GLY B:229 , ARG B:230 , ASP B:254 , HIS B:277 , ALA B:279 , OXL B:401 , HOH B:505 , HOH B:534 , HOH B:543 , HOH B:552 , HOH B:562 , HOH B:606 , HOH B:610 , HOH B:630 , HOH B:641 , HOH B:651 , HOH B:673binding site for residue NDP B 402
08AC8SOFTWAREARG A:141 , VAL B:95 , THR B:285 , ALA B:288 , HOH B:511 , HOH B:528binding site for residue GOL B 403
09AC9SOFTWAREASN B:13 , ARG B:286 , HOH B:713 , HOH B:766binding site for residue CL B 404
10AD1SOFTWAREALA B:191 , GLU B:192 , VAL B:194 , ALA B:218 , LEU B:219 , HOH B:725binding site for residue NA B 405
11AD2SOFTWAREGLY C:71 , VAL C:72 , GLY C:73 , LEU C:96 , ARG C:230 , HIS C:277 , NDP C:402 , HOH C:503 , HOH C:621binding site for residue OXL C 401
12AD3SOFTWAREVAL C:72 , VAL C:100 , PHE C:148 , LEU C:150 , GLY C:151 , ARG C:152 , ILE C:153 , THR C:172 , ARG C:173 , THR C:174 , ILE C:200 , VAL C:201 , PRO C:202 , SER C:206 , THR C:207 , VAL C:228 , GLY C:229 , ARG C:230 , ASP C:254 , HIS C:277 , ALA C:279 , OXL C:401 , HOH C:502 , HOH C:503 , HOH C:504 , HOH C:506 , HOH C:524 , HOH C:545 , HOH C:569 , HOH C:577 , HOH C:594 , HOH C:613 , HOH C:617 , HOH C:618 , HOH C:626 , HOH C:629 , HOH C:647 , HOH C:657binding site for residue NDP C 402
13AD4SOFTWAREASN C:13 , ARG C:286 , HOH C:766binding site for residue CL C 403
14AD5SOFTWAREALA C:191 , GLU C:192 , VAL C:194 , ALA C:218 , LEU C:219 , HOH C:778binding site for residue NA C 404
15AD6SOFTWAREGLY D:71 , VAL D:72 , GLY D:73 , LEU D:96 , ARG D:230 , HIS D:277 , NDP D:402 , HOH D:506 , HOH D:519 , HOH D:559binding site for residue OXL D 401
16AD7SOFTWAREVAL D:72 , VAL D:100 , PHE D:148 , LEU D:150 , GLY D:151 , ARG D:152 , ILE D:153 , THR D:172 , ARG D:173 , THR D:174 , ILE D:200 , VAL D:201 , PRO D:202 , SER D:206 , THR D:207 , VAL D:228 , GLY D:229 , ARG D:230 , ASP D:254 , HIS D:277 , ALA D:279 , OXL D:401 , HOH D:505 , HOH D:506 , HOH D:509 , HOH D:547 , HOH D:549 , HOH D:565 , HOH D:566 , HOH D:578 , HOH D:583 , HOH D:591 , HOH D:628 , HOH D:645 , HOH D:687binding site for residue NDP D 402
17AD8SOFTWAREVAL D:95 , THR D:285 , ALA D:288 , HOH D:609binding site for residue GOL D 403
18AD9SOFTWAREASN D:13 , ARG D:286 , HOH D:824binding site for residue CL D 404
19AE1SOFTWAREALA D:191 , GLU D:192 , VAL D:194 , ALA D:218 , LEU D:219 , HOH D:754binding site for residue NA D 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5V7G)

(-) 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 5V7G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V7G)

(-) Exons   (0, 0)

(no "Exon" information available for 5V7G)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhh.eeeee...hhhhhhhhhh...eeee....hhhhhh......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee..hhhhhhhhhhhhh...eeeee..........ee..hhhhhhhhh.eeee............hhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v7g A   3 RPRILVPGKINPRVLERLPEMFETVRIERADAALVTADMRDVSGIAVSGKLPVPLMDAFPSLEIVANFGVGYDGVDVSRAAARGIVVTNTPDVLTEEVADTAIGLLLNTLRLLPQAEQWLRQGRWVREGAFPLSPLSLRGRTVGLFGLGRIGLAIARRLEAFGVSIAYHTRTPREGLGFTYHPTLVGMAEAVDTLIVIVPGTASTLKAVNADVLSALGPKGVLINVGRGSTVDEAALVTALQNGTIAGAGLDVFENEPNVPEALLSFPNVSLLPHVASASVVTRNAMSDLVVDNLKAWFSTGEALTPVAETPFRRRA 319
                                    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       


Chain B from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhh.eeeee...hhhhhhhhhh...eeee....hhhhhh......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee..hhhhhhhhhhhhh...eeeee..........ee..hhhhhhhhh.eeee............hhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v7g B   3 RPRILVPGKINPRVLERLPEMFETVRIERADAALVTADMRDVSGIAVSGKLPVPLMDAFPSLEIVANFGVGYDGVDVSRAAARGIVVTNTPDVLTEEVADTAIGLLLNTLRLLPQAEQWLRQGRWVREGAFPLSPLSLRGRTVGLFGLGRIGLAIARRLEAFGVSIAYHTRTPREGLGFTYHPTLVGMAEAVDTLIVIVPGTASTLKAVNADVLSALGPKGVLINVGRGSTVDEAALVTALQNGTIAGAGLDVFENEPNVPEALLSFPNVSLLPHVASASVVTRNAMSDLVVDNLKAWFSTGEALTPVAETPFRRRA 319
                                    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       


Chain C from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhh.eeeee...hhhhhhhhhh...eeee....hhhhhh......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee..hhhhhhhhhhhhh...eeeee..........ee..hhhhhhhhh.eeee............hhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v7g C   3 RPRILVPGKINPRVLERLPEMFETVRIERADAALVTADMRDVSGIAVSGKLPVPLMDAFPSLEIVANFGVGYDGVDVSRAAARGIVVTNTPDVLTEEVADTAIGLLLNTLRLLPQAEQWLRQGRWVREGAFPLSPLSLRGRTVGLFGLGRIGLAIARRLEAFGVSIAYHTRTPREGLGFTYHPTLVGMAEAVDTLIVIVPGTASTLKAVNADVLSALGPKGVLINVGRGSTVDEAALVTALQNGTIAGAGLDVFENEPNVPEALLSFPNVSLLPHVASASVVTRNAMSDLVVDNLKAWFSTGEALTPVAETPFRRRA 319
                                    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       


Chain D from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhh.eeeee...hhhhhhhhhh...eeee....hhhhhh......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee..hhhhhhhhhhhhh...eeeee..........ee..hhhhhhhhh.eeee............hhhhhhhhh...eeee..hhhhhhhhhhhhhhhh....eeee.........hhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v7g D   3 RPRILVPGKINPRVLERLPEMFETVRIERADAALVTADMRDVSGIAVSGKLPVPLMDAFPSLEIVANFGVGYDGVDVSRAAARGIVVTNTPDVLTEEVADTAIGLLLNTLRLLPQAEQWLRQGRWVREGAFPLSPLSLRGRTVGLFGLGRIGLAIARRLEAFGVSIAYHTRTPREGLGFTYHPTLVGMAEAVDTLIVIVPGTASTLKAVNADVLSALGPKGVLINVGRGSTVDEAALVTALQNGTIAGAGLDVFENEPNVPEALLSFPNVSLLPHVASASVVTRNAMSDLVVDNLKAWFSTGEALTPVAETPFRRRA 319
                                    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
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 5V7G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V7G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V7G)

(-) Gene Ontology  (4, 4)

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  5v7g
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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 5v72 5v7n

(-) Related Entries Specified in the PDB File

5j23 SMGHRB, COMPLEX WITH 2'-PHOSPHO-ADP-RIBOSE
5uog SMGHRB, APO FORM
5v6q SMGHRB, COMPLEX WITH NADP AND MALONATE
5v72 SMGHRB, COMPLEX WITH CITRATE
5v7n SMGHRB, COMPLEX WITH NADP AND 2-KETO-D-GLUCONIC ACID RELATED ID: NYSGRC-012132 RELATED DB: TARGETTRACK