Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A 2-HYDROXY-3-OXOPROPIONATE REDUCTASE FROM POLAROMONAS SP. JS666
 
Authors :  R. Agarwal, S. Chamala, B. Evans, R. Foti, A. Gizzi, B. Hillerich, A. Kar J. Lafleur, R. Seidel, G. Villigas, W. Zencheck, S. C. Almo, S. Swamina York Structural Genomics Research Consortium (Nysgrc)
Date :  06 Feb 12  (Deposition) - 15 Feb 12  (Release) - 15 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, 2-Hydroxy-3-Oxopropionate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Agarwal, S. C. Almo, S. Swaminathan
Crystal Structure Of A 2-Hydroxy-3-Oxopropionate Reductase From Polaromonas Sp. Js666
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 2-HYDROXY-3-OXOPROPIONATE REDUCTASE
    Chains: A, B
    EC Number: 1.1.1.60
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: 2-HYDROXY-3-OXOPROPIONATE REDUCTASE
    Gene: BPRO_1712
    Organism Scientific: POLAROMONAS SP. JS666
    Organism Taxid: 296591
    Strain: JS666 / ATCC BAA-500

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 22)

Asymmetric/Biological Unit (2, 22)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:38 , THR A:39 , GLY A:40 , ASN A:61 , ARG A:62 , THR A:63BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWAREGLY B:38 , THR B:39 , ASN B:61 , ARG B:62 , THR B:63 , ARG B:66BINDING SITE FOR RESIDUE SO4 B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DLL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DLL)

(-) 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:288
 aligned with Q12CU4_POLSJ | Q12CU4 from UniProtKB/TrEMBL  Length:298

    Alignment length:288
                                    16        26        36        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        
         Q12CU4_POLSJ     7 PYARKITFLGTGSMGLPMARRLCEAGYALQVWNRTPARAASLAALGATIHEQARAAARDADIVVSMLENGAVVQDVLFAQGVAAAMKPGSLFLDMASITPREARDHAARLGALGIAHLDTPVSGGTVGAEQGTLVIMAGGKPADFERSLPLLKVFGRATHVGPHGSGQLTKLANQMIVGITIGAVAEALLFATKGGADMAKVKEAITGGFADSRVLQLHGQRMVERDFAPRARLSIQLKDMRNALATAQEIGFDAPITGLFEQLYAEGVEHGLTDLDQSGLFVELASR 294
               SCOP domains d4dlla1 A:29-190 automated matches                                                                                                                                d4dlla2 A:191-316 automated matches                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhh...eee.hhhhhhh...eeee...hhhhhhhhhh..hhhhhh....eeee....hhhhhhhhhhhhhhh..eeee..eehhhhhhhhh.eeeeee.hhhhhhhhhhhhhhheeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dll A  29 PYARKITFLGTGSmGLPmARRLCEAGYALQVWNRTPARAASLAALGATIHEQARAAARDADIVVSmLENGAVVQDVLFAQGVAAAmKPGSLFLDmASITPREARDHAARLGALGIAHLDTPVSGGTVGAEQGTLVImAGGKPADFERSLPLLKVFGRATHVGPHGSGQLTKLANQmIVGITIGAVAEALLFATKGGADmAKVKEAITGGFADSRVLQLHGQRmVERDFAPRARLSIQLKDmRNALATAQEIGFDAPITGLFEQLYAEGVEHGLTDLDQSGLFVELASR 316
                                    38   |   |48        58        68        78        88     |  98       108     | 118    |  128       138       148       158      |168       178       188       198     | 208       218       228       238       248  |    258       268|      278       288       298       308        
                                        42-MSE                                              94-MSE             114-MSE  123-MSE                                   165-MSE                                204-MSE                227-MSE                 251-MSE           269-MSE                                           
                                            46-MSE                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:285
 aligned with Q12CU4_POLSJ | Q12CU4 from UniProtKB/TrEMBL  Length:298

    Alignment length:287
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       
         Q12CU4_POLSJ    10 RKITFLGTGSMGLPMARRLCEAGYALQVWNRTPARAASLAALGATIHEQARAAARDADIVVSMLENGAVVQDVLFAQGVAAAMKPGSLFLDMASITPREARDHAARLGALGIAHLDTPVSGGTVGAEQGTLVIMAGGKPADFERSLPLLKVFGRATHVGPHGSGQLTKLANQMIVGITIGAVAEALLFATKGGADMAKVKEAITGGFADSRVLQLHGQRMVERDFAPRARLSIQLKDMRNALATAQEIGFDAPITGLFEQLYAEGVEHGLTDLDQSGLFVELASRNG 296
               SCOP domains d4dllb1   B:32-190 automated matches                                                                                                                           d4dllb2 B:191-318 automated matches                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..--.hhhhhhhhhhh..eeeee..hhhhhhhhhhhh.ee..hhhhhhh...eeee...hhhhhhhhhhh.hhhhhh....eeee....hhhhhhhhhhhhhhh..eeee..ee.hhhhhhh..eeeeee.hhhhhhhhhhhhhhheeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dll B  32 RKITFLGT--mGLPmARRLCEAGYALQVWNRTPARAASLAALGATIHEQARAAARDADIVVSmLENGAVVQDVLFAQGVAAAmKPGSLFLDmASITPREARDHAARLGALGIAHLDTPVSGGTVGAEQGTLVImAGGKPADFERSLPLLKVFGRATHVGPHGSGQLTKLANQmIVGITIGAVAEALLFATKGGADmAKVKEAITGGFADSRVLQLHGQRmVERDFAPRARLSIQLKDmRNALATAQEIGFDAPITGLFEQLYAEGVEHGLTDLDQSGLFVELASRNG 318
                                   | -|   |   51        61        71        81        91  |    101       111  |    121 |     131       141       151       161   |   171       181       191       201  |    211       221     | 231       241       251       261       271       281       291       301       311       
                                  39  |   |                                              94-MSE             114-MSE  123-MSE                                   165-MSE                                204-MSE                227-MSE                 251-MSE           269-MSE                                             
                                     42-MSE                                                                                                                                                                                                                                                                                
                                         46-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DLL)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q12CU4_POLSJ | Q12CU4)
molecular function
    GO:0008679    2-hydroxy-3-oxopropionate reductase activity    Catalysis of the reaction: (R)-glycerate + NADP+ = 2-hydroxy-3-oxopropanoate + NADPH + H+.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004616    phosphogluconate dehydrogenase (decarboxylating) activity    Catalysis of the reaction: 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH + H+.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4dll)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4dll
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q12CU4_POLSJ | Q12CU4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.1.1.60
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q12CU4_POLSJ | Q12CU4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4DLL)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4DLL)