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(-) Description

Title :  STRUCTURE OF PROBABLE MANDELATE RACEMASE (AALAA1DRAFT_2112) FROM ALICYCLOBACILLUS ACIDOCALDARIUS
 
Authors :  U. A. Ramagopal, R. Toro, S. K. Burley, S. C. Almo, New York Sgx Resear For Structural Genomics (Nysgxrc)
Date :  02 Feb 11  (Deposition) - 27 Apr 11  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-2, Isomerase, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. A. Ramagopal, R. Toro, S. K. Burley, S. C. Almo
Structure Of Probable Mandelate Racemase (Aalaa1Draft_2112) From Alicyclobacillus Acidocaldarius
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-PSGX4(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AALAA1DRAFT_2112
    Organism Scientific: ALICYCLOBACILLUS ACIDOCALDARIUS LAA1
    Organism Taxid: 543302

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric/Biological Unit (2, 21)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2SO45Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:104 , SER A:250 , VAL A:251 , ARG A:252 , ARG A:281BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWAREARG A:101 , GLY A:102 , ARG A:104 , ARG A:252 , HOH A:426BINDING SITE FOR RESIDUE SO4 A 402
3AC3SOFTWARETRP A:64 , HIS A:69 , HIS A:383BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWAREARG A:209 , ARG A:239 , HOH A:436 , HOH A:479BINDING SITE FOR RESIDUE SO4 A 404
5AC5SOFTWAREARG B:104 , VAL B:251 , ARG B:252 , ARG B:281BINDING SITE FOR RESIDUE SO4 B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QLD)

(-) Exons   (0, 0)

(no "Exon" information available for 3QLD)

(-) 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:383
 aligned with B7DSY7_9BACL | B7DSY7 from UniProtKB/TrEMBL  Length:379

    Alignment length:383
                                                                                                                                                                                                                                                                                                                                                                                                                    379    
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370        |-   
         B7DSY7_9BACL     1 MIQTCVLHRLSLPLKFPMRTAHGHIREKQAILVQLVDADGIEGWSECVALAEPTYTEECTDTAWVMLVHHLVPRFARWLRAASQDQDVDPRTVCEALRDVRGNRMSVAAIEMAVWDWYAARTGQPLVGLLGGGRDRVEVSATLGMSESLDVLIQSVDAAVEQGFRRVKLKIAPGRDRAAIKAVRLRYPDLAIAADANGSYRPEDAPVLRQLDAYDLQFIEQPLPEDDWFDLAKLQASLRTPVCLDESVRSVRELKLTARLGAARVLNVKPGRLGGFGATLRALDVAGEAGMAAWVGGMYETGVGRVHGLIAAALPLMRYATDLGPSDRYFEQDVLKEPIAFVEPGVIQVPQCAGVADWVDRDAVRRFSTATWSVDLRTL----   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeeee....eeeeeeeeeeeeee....eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhh.....eee.eeee....hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...ee......hhhhhhhhhhhh...eee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh...........hhhhh................eee......hhhhhhhhhhhhheeeeeeee.....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qld A   1 SLQTCVLHRLSLPLKFPmRTAHGHIREKQAILVQLVDADGIEGWSECVALAEPTYTEECTDTAWVmLVHHLVPRFARWLRAASQDQDVDPRTVCEALRDVRGNRmSVAAIEmAVWDWYAARTGQPLVGLLGGGRDRVEVSATLGmSESLDVLIQSVDAAVEQGFRRVKLKIAPGRDRAAIKAVRLRYPDLAIAADANGSYRPEDAPVLRQLDAYDLQFIEQPLPEDDWFDLAKLQASLRTPVCLDESVRSVRELKLTARLGAARVLNVKPGRLGGFGATLRALDVAGEAGmAAWVGGmYETGVGRVHGLIAAALPLmRYATDLGPSDRYFEQDVLKEPIAFVEPGVIQVPQCAGVADWVDRDAVRRFSTATWSVDLRTLEGHH 383
                                    10       |20        30        40        50        60     |  70        80        90       100    |  110 |     120       130       140    |  150       160       170       180       190       200       210       220       230       240       250       260       270       280       290|      300       310      |320       330       340       350       360       370       380   
                                            18-MSE                                          66-MSE                                105-MSE  |                              145-MSE                                                                                                                                           291-MSE  |                317-MSE                                                              
                                                                                                                                         112-MSE                                                                                                                                                                                   298-MSE                                                                                 


Chain B from PDB  Type:PROTEIN  Length:374
 aligned with B7DSY7_9BACL | B7DSY7 from UniProtKB/TrEMBL  Length:379

    Alignment length:378
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370        
         B7DSY7_9BACL     1 MIQTCVLHRLSLPLKFPMRTAHGHIREKQAILVQLVDADGIEGWSECVALAEPTYTEECTDTAWVMLVHHLVPRFARWLRAASQDQDVDPRTVCEALRDVRGNRMSVAAIEMAVWDWYAARTGQPLVGLLGGGRDRVEVSATLGMSESLDVLIQSVDAAVEQGFRRVKLKIAPGRDRAAIKAVRLRYPDLAIAADANGSYRPEDAPVLRQLDAYDLQFIEQPLPEDDWFDLAKLQASLRTPVCLDESVRSVRELKLTARLGAARVLNVKPGRLGGFGATLRALDVAGEAGMAAWVGGMYETGVGRVHGLIAAALPLMRYATDLGPSDRYFEQDVLKEPIAFVEPGVIQVPQCAGVADWVDRDAVRRFSTATWSVDLRT 378
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --MR_MLE_N-3qldB01 B:3-131                                                                                                         -----------------------------------------------MR_MLE-3qldB03 B:179-245                                           ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --MR_MLE_N-3qldB02 B:3-131                                                                                                         -----------------------------------------------MR_MLE-3qldB04 B:179-245                                           ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeee....eeeeee...........hhhhhhhhhhhhhhhhhhhhhh..----..hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhhh....eee.eeee....hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...ee......hhhhhhhhhhh....eee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh............hhhhh................eee......hhhhhhhhhhhhheeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qld B   1 SLQTCVLHRLSLPLKFPmRTAHGHIREKQAILVQLVDADGIEGWSECVALAEPTYTEECTDTAWVmLVHHLVPRFARWLRAA----DVDPRTVCEALRDVRGNRmSVAAIEmAVWDWYAARTGQPLVGLLGGGRDRVEVSATLGmSESLDVLIQSVDAAVEQGFRRVKLKIAPGRDRAAIKAVRLRYPDLAIAADANGSYRPEDAPVLRQLDAYDLQFIEQPLPEDDWFDLAKLQASLRTPVCLDESVRSVRELKLTARLGAARVLNVKPGRLGGFGATLRALDVAGEAGmAAWVGGmYETGVGRVHGLIAAALPLmRYATDLGPSDRYFEQDVLKEPIAFVEPGVIQVPQCAGVADWVDRDAVRRFSTATWSVDLRT 378
                                    10       |20        30        40        50        60     |  70        80 |    | 90       100    |  110 |     120       130       140    |  150       160       170       180       190       200       210       220       230       240       250       260       270       280       290|      300       310      |320       330       340       350       360       370        
                                            18-MSE                                          66-MSE          82   87               105-MSE  |                              145-MSE                                                                                                                                           291-MSE  |                317-MSE                                                         
                                                                                                                                         112-MSE                                                                                                                                                                                   298-MSE
   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 3QLD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QLD)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Enolase_N (69)
(-)
Clan: Enolase_TIM (82)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B7DSY7_9BACL | B7DSY7)
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:0016836    hydro-lyase activity    Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    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:0009234    menaquinone biosynthetic process    The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
    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.

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