Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
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 PUTATIVE MANDELATE RACEMASE/MUCONATE LACTONIZING PROTEIN FROM CLOSTRIDIUM BEIJERINCKII NCIMB 8052
 
Authors :  V. N. Malashkevich, R. Toro, C. Morano, J. M. Sauder, S. K. Burley, S. C. A York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  03 Apr 09  (Deposition) - 14 Apr 09  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Structural Genomics, Crystal Structure, Protein Structure Initiative, Mandelate Racemase/Muconate Lactonizing Protein, Clostridium Beijerinckii Ncimb 8052, Nysgxrc, Enolase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, R. Toro, C. Morano, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Putative Mandelate Racemase/Muconate Lactonizing Protein From Clostridium Beijerinckii Ncimb 805
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MANDELATE RACEMASE/MUCONATE LACTONIZING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CBEI_4837
    Organism Common: CLOSTRIDIUM ACETOBUTYLICUM
    Organism Scientific: CLOSTRIDIUM BEIJERINCKII
    Organism Taxid: 290402
    Strain: NCIMB 8052

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:207 , GLU A:233 , GLU A:259 , HOH B:509 , HOH B:545 , HOH B:746BINDING SITE FOR RESIDUE MG A 500
2AC2SOFTWAREASP B:207 , GLU B:233 , GLU B:259 , HOH B:495 , HOH B:611 , HOH B:655BINDING SITE FOR RESIDUE MG B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GY1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GY1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GY1)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MR_MLE_1PS00908 Mandelate racemase / muconate lactonizing enzyme family signature 1.IMAND_CLOB889-114
 		  2A:91-116
B:91-116
Biological Unit 1 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MR_MLE_1PS00908 Mandelate racemase / muconate lactonizing enzyme family signature 1.IMAND_CLOB889-114
 		  8A:91-116
B:91-116

(-) Exons   (0, 0)

(no "Exon" information available for 3GY1)

(-) 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:387
 aligned with IMAND_CLOB8 | A6M2W4 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:403
                             1                                                                                                                                                                                                                                                                                                                                                                                                           399   
                             |       9        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       299       309       319       329       339       349       359       369       379       389       399   
          IMAND_CLOB8     - -MEPTIITDVLCYITKPDRHNLVVVKVETNKGIYGLGCATFQQRPKAVSLVVSEYLKPILIGRDANNIEDLWQMMMVNSYWRNGPILNNAISGVDMALWDIKGKLANMPLYQLFGGKSRDAIAAYTHAVADNLEDLYTEIDEIRKKGYQHIRCQLGFYGGNSSEFHTTDNPTQGSYFDQDEYMRTTVSMFSSLREKYGYKFHILHDVHERLFPNQAVQFAKDVEKYKPYFIEDILPPDQNEWLGQIRSQTSTPLATGELFNNPMEWKSLIANRQVDFIRCHVSQIGGITPALKLGSLCAAFGVRIAWHTPSDITPIGVAVNIHLNINLHNAAIQENIEINDNTRCVFSGIPEAKNGFFYPIESPGIGVDIDENEIIKYPVEYRPHEWTQSRIPDGTIVTP---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3gy1A01 A:2-110,A:364-404 Enolase-like, N-terminal domain                                                    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3gy1A01 A:2-110,A:364-404                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee......eeeeeeee....eeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.......eeeeeeeee.hhhhhhhhhhhhhhh...eeeeee..----------------.ee.hhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhh.....eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhh..ee........hhhhhhhhhhhhhhh.....ee....hhhhhhhee........ee..........eehhhhhh......hhh.eeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------MR_MLE_1  PDB: A:91-116   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gy1 A   2 SLEPTIITDVLCYITKPDRHNLVVVKVETNKGIYGLGCATFQQRPKAVSLVVSEYLKPILIGRDANNIEDLWQMMMVNSYWRNGPILNNAISGVDMALWDIKGKLANMPLYQLFGGKSRDAIAAYTHAVADNLEDLYTEIDEIRKKGYQHIRCQLGF----------------GSYFDQDEYMRTTVSMFSSLREKYGYKFHILHDVHERLFPNQAVQFAKDVEKYKPYFIEDILPPDQNEWLGQIRSQTSTPLATGELFNNPMEWKSLIANRQVDFIRCHVSQIGGITPALKLGSLCAAFGVRIAWHTPSDITPIGVAVNIHLNINLHNAAIQENIEINDNTRCVFSGIPEAKNGFFYPIESPGIGVDIDENEIIKYPVEYRPHEWTQSRIPDGTIVTEGHH 404
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      |  -         -   |   181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401   
                                                                                                                                                                                      158              175                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:388
 aligned with IMAND_CLOB8 | A6M2W4 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:403
                             1                                                                                                                                                                                                                                                                                                                                                                                                           399   
                             |       9        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       299       309       319       329       339       349       359       369       379       389       399   
          IMAND_CLOB8     - -MEPTIITDVLCYITKPDRHNLVVVKVETNKGIYGLGCATFQQRPKAVSLVVSEYLKPILIGRDANNIEDLWQMMMVNSYWRNGPILNNAISGVDMALWDIKGKLANMPLYQLFGGKSRDAIAAYTHAVADNLEDLYTEIDEIRKKGYQHIRCQLGFYGGNSSEFHTTDNPTQGSYFDQDEYMRTTVSMFSSLREKYGYKFHILHDVHERLFPNQAVQFAKDVEKYKPYFIEDILPPDQNEWLGQIRSQTSTPLATGELFNNPMEWKSLIANRQVDFIRCHVSQIGGITPALKLGSLCAAFGVRIAWHTPSDITPIGVAVNIHLNINLHNAAIQENIEINDNTRCVFSGIPEAKNGFFYPIESPGIGVDIDENEIIKYPVEYRPHEWTQSRIPDGTIVTP---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3gy1B01 B:2-110,B:364-404 Enolase-like, N-terminal domain                                                    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3gy1B01 B:2-110,B:364-404                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee......eeeeeeee....eeeee.....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.......eeeeeeeee.hhhhhhhhhhhhhhh...eeeeee..---------------..ee.hhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhh.....eee.....hhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhh..ee........hhhhhhhhhhhhhhh.....ee....hhhhhhhee........ee..........eehhhhhh......hhh.eeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------MR_MLE_1  PDB: B:91-116   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gy1 B   2 SLEPTIITDVLCYITKPDRHNLVVVKVETNKGIYGLGCATFQQRPKAVSLVVSEYLKPILIGRDANNIEDLWQMMMVNSYWRNGPILNNAISGVDMALWDIKGKLANMPLYQLFGGKSRDAIAAYTHAVADNLEDLYTEIDEIRKKGYQHIRCQLGF---------------QGSYFDQDEYMRTTVSMFSSLREKYGYKFHILHDVHERLFPNQAVQFAKDVEKYKPYFIEDILPPDQNEWLGQIRSQTSTPLATGELFNNPMEWKSLIANRQVDFIRCHVSQIGGITPALKLGSLCAAFGVRIAWHTPSDITPIGVAVNIHLNINLHNAAIQENIEINDNTRCVFSGIPEAKNGFFYPIESPGIGVDIDENEIIKYPVEYRPHEWTQSRIPDGTIVTEGHH 404
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      |  -         -  |    181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401   
                                                                                                                                                                                      158             174
   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  (0, 0)

(no "SCOP Domain" information available for 3GY1)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GY1)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IMAND_CLOB8 | A6M2W4)
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: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.
biological process
    GO:0009063    cellular amino acid catabolic process    The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
    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 ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3gy1)
 
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
  3gy1
    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
  IMAND_CLOB8 | A6M2W4
    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
  IMAND_CLOB8 | A6M2W4
    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
        IMAND_CLOB8 | A6M2W4: 3s47

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3GY1)