Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME FROM ROSEOVARIUS SP. HTCC2601
 
Authors :  J. B. Bonanno, M. Rutter, K. T. Bain, C. Lau, V. Sridhar, D. Smith, S. Wass J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center Structural Genomics (Nysgxrc)
Date :  23 Apr 07  (Deposition) - 08 May 07  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Structural Genomics, Isomerase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Zhao, R. Kumar, A. Sakai, M. W. Vetting, B. M. Wood, S. Brown, J. B. Bonanno, B. S. Hillerich, R. D. Seidel, P. C. Babbitt, S. C. Almo, J. V. Sweedler, J. A. Gerlt, J. E. Cronan, M. P. Jacobson
Discovery Of New Enzymes And Metabolic Pathways By Using Structure And Genome Context.
Nature V. 502 698 2013
PubMed-ID: 24056934  |  Reference-DOI: 10.1038/NATURE12576

(-) Compounds

Molecule 1 - MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Gene: R2601_01638
    Organism Scientific: ROSEOVARIUS SP.
    Organism Taxid: 314265
    Strain: HTCC2601

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 19)

Asymmetric Unit (2, 19)
No.NameCountTypeFull Name
1MG5Ligand/IonMAGNESIUM ION
2MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 56)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE56Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:1056 , HOH A:1250 , HOH A:1258 , HOH B:1038 , HOH B:1074 , HOH B:1163BINDING SITE FOR RESIDUE MG A 901
2AC2SOFTWAREASP A:193 , ASN A:195 , GLU A:218 , ASP A:241 , HOH A:913 , HOH A:965 , HOH A:1239BINDING SITE FOR RESIDUE MG A 902
3AC3SOFTWAREHIS A:235 , HOH A:945 , HOH A:1118BINDING SITE FOR RESIDUE MG A 903
4AC4SOFTWAREASP B:193 , GLU B:218 , ASP B:241 , HOH B:921 , HOH B:933 , HOH B:1005BINDING SITE FOR RESIDUE MG B 904
5AC5SOFTWAREHIS B:235 , HOH B:963 , HOH B:1134BINDING SITE FOR RESIDUE MG B 905

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PMQ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:18 -Pro A:19
2Gly B:18 -Pro B:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PMQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PMQ)

(-) Exons   (0, 0)

(no "Exon" information available for 2PMQ)

(-) 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:367
 aligned with HPBD_PELBH | Q0FPQ4 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:367
                                                                                                                                                                                                                                                                                                                                                                                                       367 
                                    11        21        31        41        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       321       331       341       351       361     | 
           HPBD_PELBH     2 KIAEIQLFQHDLPVVNGPYRIASGDVWSLTTTIVKIIAEDGTIGWGETCPVGPTYAEAHAGGALAALEVLASGLAGAEALPLPLHTRMDSLLCGHNYAKSALDIAVHDLWGKRLGVPVHELLGGALTDSVSSYYSLGVMEPDEAARQALEKQREGYSRLQVKLGARPIEIDIEAIRKVWEAVRGTGIALAADGNRGWTTRDALRFSRECPDIPFVMEQPCNSFEDLEAIRPLCHHALYMDEDGTSLNTVITAAATSLVDGFGMKVSRIGGLQHMRAFRDFCAARNLPHTCDDAWGGDIVSAACTHIASTVLPRLMEGAWLAQPYVAEHYDAENGVRIEGGRIRVPQGPGLGLTIDPERFGPPLFSA-   -
               SCOP domains d2pmqa1 A:2-125 automated matches                                                                                           d2pmqa2 A:126-368 automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains 2pmqA01 A:2-116,A:351-364 Enolase-like, N-terminal domain                                                          2pmqA02 A:117-350 Enolase superfamily                                                                                                                                                                                                     2pmqA01       ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee..............eeeeeeeeeee....eeeeee..........hhhhhhhhhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhh......eee.eeee...hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh....eeee....hhhhhhhhhhhh...eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhhhhh.eee...hhhhh...........ee..eee....................eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pmq A   2 KIAEIQLFQHDLPVVNGPYRIASGDVWSLTTTIVKIIAEDGTIGWGETCPVGPTYAEAHAGGALAALEVLASGLAGAEALPLPLHTRmDSLLCGHNYAKSALDIAVHDLWGKRLGVPVHELLGGALTDSVSSYYSLGVmEPDEAARQALEKQREGYSRLQVKLGARPIEIDIEAIRKVWEAVRGTGIALAADGNRGWTTRDALRFSRECPDIPFVmEQPCNSFEDLEAIRPLCHHALYmDEDGTSLNTVITAAATSLVDGFGmKVSRIGGLQHmRAFRDFCAARNLPHTCDDAWGGDIVSAACTHIASTVLPRLmEGAWLAQPYVAEHYDAENGVRIEGGRIRVPQGPGLGLTIDPERFGPPLFSAE 368
                                    11        21        31        41        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    |  321       331       341       351       361       
                                                                                                                  89-MSE                                            140-MSE                                                                      217-MSE                240-MSE                 264-MSE    275-MSE                                  316-MSE                                                


Chain B from PDB  Type:PROTEIN  Length:374
 aligned with HPBD_PELBH | Q0FPQ4 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:374
                                                                                                                                                                                                                                                                                                                                                                                                       367        
                                    11        21        31        41        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       321       331       341       351       361     |   -    
           HPBD_PELBH     2 KIAEIQLFQHDLPVVNGPYRIASGDVWSLTTTIVKIIAEDGTIGWGETCPVGPTYAEAHAGGALAALEVLASGLAGAEALPLPLHTRMDSLLCGHNYAKSALDIAVHDLWGKRLGVPVHELLGGALTDSVSSYYSLGVMEPDEAARQALEKQREGYSRLQVKLGARPIEIDIEAIRKVWEAVRGTGIALAADGNRGWTTRDALRFSRECPDIPFVMEQPCNSFEDLEAIRPLCHHALYMDEDGTSLNTVITAAATSLVDGFGMKVSRIGGLQHMRAFRDFCAARNLPHTCDDAWGGDIVSAACTHIASTVLPRLMEGAWLAQPYVAEHYDAENGVRIEGGRIRVPQGPGLGLTIDPERFGPPLFSA--------   -
               SCOP domains d2pmqb1 B:2-125 automated matches                                                                                           d2pmqb2 B:126-375 automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains 2pmqB01 B:2-116,B:351-364 Enolase-like, N-terminal domain                                                          2pmqB02 B:117-350 Enolase superfamily                                                                                                                                                                                                     2pmqB01       ----------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee..............eeeeeeeeeee....eeeeee..........hhhhhhhhhhhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhh......eee.eeee...hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh....eeee....hhhhhhhhhhhh...eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhhhhh.eee...hhhhh...........ee..eee....................eeee..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pmq B   2 KIAEIQLFQHDLPVVNGPYRIASGDVWSLTTTIVKIIAEDGTIGWGETCPVGPTYAEAHAGGALAALEVLASGLAGAEALPLPLHTRmDSLLCGHNYAKSALDIAVHDLWGKRLGVPVHELLGGALTDSVSSYYSLGVmEPDEAARQALEKQREGYSRLQVKLGARPIEIDIEAIRKVWEAVRGTGIALAADGNRGWTTRDALRFSRECPDIPFVmEQPCNSFEDLEAIRPLCHHALYmDEDGTSLNTVITAAATSLVDGFGmKVSRIGGLQHmRAFRDFCAARNLPHTCDDAWGGDIVSAACTHIASTVLPRLmEGAWLAQPYVAEHYDAENGVRIEGGRIRVPQGPGLGLTIDPERFGPPLFSAEGHHHHHH 375
                                    11        21        31        41        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    |  321       331       341       351       361       371    
                                                                                                                  89-MSE                                            140-MSE                                                                      217-MSE                240-MSE                 264-MSE    275-MSE                                  316-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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PMQ)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HPBD_PELBH | Q0FPQ4)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0036361    racemase activity, acting on amino acids and derivatives    Catalysis of the interconversion of the two enantiomers of a chiral amino acid or amino acid derivative.
    GO:0016855    racemase and epimerase activity, acting on amino acids and derivatives    Catalysis of a reaction that alters the configuration of one or more chiral centers in an amino acid.
biological process
    GO:0006579    amino-acid betaine catabolic process    The chemical reactions and pathways resulting in the breakdown of any betaine, the N-trimethyl derivative of an amino acid.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

 Visualization

(-) Interactive Views

Asymmetric 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:18 - Pro A:19   [ RasMol ]  
    Gly B:18 - Pro B:19   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  2pmq
    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
  HPBD_PELBH | Q0FPQ4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  HPBD_PELBH | Q0FPQ4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        HPBD_PELBH | Q0FPQ4: 4h2h

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2PMQ)