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(-) Description

Title :  CRYSTAL STRUCTURE OF A CORC_HLYC DOMAIN FROM HAEMOPHILUS DUCREYI
 
Authors :  M. E. Cuff, L. Volkart, S. Moy, A. Joachimiak, Midwest Center For Str Genomics (Mcsg)
Date :  12 Mar 07  (Deposition) - 22 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Haemophilus Ducreyi, Corc_hlyc, Pfam: Pf03471, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Cuff, L. Volkart, S. Moy, A. Joachimiak
The Structure Of A Corc_hlyc Domain From Haemophilus Ducrey
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN HD1797
    Atcc: 700724
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CORC_HLYC DOMAIN, RESIDUES 347-429
    Gene: TLYC, HD_1797
    Organism Scientific: HAEMOPHILUS DUCREYI
    Organism Taxid: 233412
    Strain: 35000HP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 26)

Asymmetric/Biological Unit (5, 26)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION
4MLY12Mod. Amino AcidN-DIMETHYL-LYSINE
5MSE11Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:252 , ASP B:66 , THR B:67 , GLU B:68BINDING SITE FOR RESIDUE MG B 301
2AC2SOFTWAREMSE B:42 , TYR B:43 , ARG B:46 , MLY B:59 , HOH B:425 , HOH B:438BINDING SITE FOR RESIDUE GOL B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P4P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P4P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P4P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P4P)

(-) Exons   (0, 0)

(no "Exon" information available for 2P4P)

(-) 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:84
 aligned with Q7VKS4_HAEDU | Q7VKS4 from UniProtKB/TrEMBL  Length:429

    Alignment length:84
                                   354       364       374       384       394       404       414       424    
         Q7VKS4_HAEDU   345 QIMRRNEDSWLIDGATPLEDVMRALNIHTFPRDENYETIGGFMMYMLRKIPKKTDFVLYDKYKFEIIDTENFRIDQLMVSFRKD 428
               SCOP domains --d2p4pa1 A:1-82 Hypothetical protein HD1797                                         SCOP domains
               CATH domains 2p4pA00 A:-1-82  [code=3.30.465.10, no name defined]                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhh............hhhhhhhhhhh.......eeee..eeeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 2p4p A  -1 NAmRRNEDSWLIDGATPLEDVmRALNIHTFPRDENYETIGGFmmYmLRkIPkkTDFVLYDkYkFEIIDTENFRIDQLmVSFRkD  82
                              |      8        18 |      28        38  || |  48 ||     58| |     68       |78  | 
                              |                 20-MSE               41-MSE |  ||      59-MLY           76-MSE| 
                              1-MSE                                   42-MSE|  ||        61-MLY              81-MLY
                                                                        44-MSE ||                               
                                                                           47-MLY                               
                                                                              50-MLY                            
                                                                               51-MLY                           


Chain B from PDB  Type:PROTEIN  Length:77
 aligned with Q7VKS4_HAEDU | Q7VKS4 from UniProtKB/TrEMBL  Length:429

    Alignment length:77
                                   361       371       381       391       401       411       421       
         Q7VKS4_HAEDU   352 DSWLIDGATPLEDVMRALNIHTFPRDENYETIGGFMMYMLRKIPKKTDFVLYDKYKFEIIDTENFRIDQLMVSFRKD 428
               SCOP domains d2p4pb_ B: Hypothetical protein HD1797                                        SCOP domains
               CATH domains 2p4pB00 B:6-82  [code=3.30.465.10, no name defined]                           CATH domains
           Pfam domains (1) CorC_HlyC-2p4pB01 B:6-81                                                    - Pfam domains (1)
           Pfam domains (2) CorC_HlyC-2p4pB02 B:6-81                                                    - Pfam domains (2)
         Sec.struct. author .eeeee...hhhhhhhhh............hhhhhhhhhhh.......eeee..eeeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 2p4p B   6 DSWLIDGATPLEDVmRALNIHTFPRDENYETIGGFmmYmLRkIPkkTDFVLYDkYkFEIIDTENFRIDQLmVSFRkD  82
                                    15    |   25        35     || 45 |  ||  55   | |  65        75|    | 
                                         20-MSE               41-MSE |  ||      59-MLY           76-MSE| 
                                                               42-MSE|  ||        61-MLY              81-MLY
                                                                 44-MSE ||                               
                                                                    47-MLY                               
                                                                       50-MLY                            
                                                                        51-MLY
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CorC_HlyC] (12)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7VKS4_HAEDU | Q7VKS4)
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:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016614    oxidoreductase activity, acting on CH-OH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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