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(-) Description

Title :  CRYSTAL STRUCTURE OF AMINOTRANSFERASE ASPB (NP_207418.1) FROM HELICOBACTER PYLORI 26695 AT 2.19 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  23 Oct 08  (Deposition) - 18 Nov 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Np_207418. 1, Aminotransferase Aspb, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Aminotransferase Class I And Ii, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Aminotransferase Aspb (Np_207418. 1) From Helicobacter Pylori 26695 At 2. 19 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AMINOTRANSFERASE ASPB
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_207418.1, HP_0624
    Organism Common: CAMPYLOBACTER PYLORI
    Organism Scientific: HELICOBACTER PYLORI 26695
    Organism Taxid: 85962
    Synonym: SOLUTE-BINDING SIGNATURE AND MITOCHONDRIAL SIGNATURE PROTEIN (ASPB)

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2MSE6Mod. Amino AcidSELENOMETHIONINE
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:54 , SER B:90 , ARG B:91 , SER B:227 , SER B:229 , ARG B:238BINDING SITE FOR RESIDUE PO4 B 376
02AC2SOFTWARESER A:90 , ARG A:91 , SER A:227 , SER A:229 , ARG A:238 , HOH A:578 , HOH A:716 , TYR B:54BINDING SITE FOR RESIDUE PO4 A 376
03AC3SOFTWAREASN A:160 , SER A:161 , ARG A:168 , LEU A:170BINDING SITE FOR RESIDUE EDO A 377
04AC4SOFTWARELYS B:180 , ASP B:356BINDING SITE FOR RESIDUE EDO B 377
05AC5SOFTWAREMSE B:1 , THR B:2BINDING SITE FOR RESIDUE EDO B 378
06AC6SOFTWAREALA B:129 , SER B:131BINDING SITE FOR RESIDUE EDO B 379
07AC7SOFTWARELEU A:133 , SER A:145 , GLU A:150 , HOH A:531BINDING SITE FOR RESIDUE EDO A 378
08AC8SOFTWAREPRO B:144 , ASN B:160 , SER B:161 , ARG B:168BINDING SITE FOR RESIDUE EDO B 380
09AC9SOFTWARETHR B:169 , LEU B:170 , SER B:171 , TYR B:307BINDING SITE FOR RESIDUE EDO B 381
10BC1SOFTWARETYR A:117 , ASN A:160 , ASN A:164 , ASP A:192 , TYR A:195 , HOH A:381BINDING SITE FOR RESIDUE EDO A 379

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Asn A:114 -Pro A:115
2Ser A:161 -Pro A:162
3Asn A:164 -Pro A:165
4Asn B:114 -Pro B:115
5Ser B:161 -Pro B:162
6Asn B:164 -Pro B:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3EZS)

(-) 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:374
 aligned with O25341_HELPY | O25341 from UniProtKB/TrEMBL  Length:375

    Alignment length:374
                             1                                                                                                                                                                                                                                                                                                                                                                                    
                             |       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    
         O25341_HELPY     - -MTFEPYPFERLRALLKEITPKKRGLDLGIGEPQFETPKFIQDALKNHTHSLNIYPKSAFEESLRAAQRGFFKRRFKIELKENELISTLGSREVLFNFPSFVLFDYQNPTIAYPNPFYQIYEGAAKFIKAKSLLMPLTKENDFTPSLNEKELQEVDLVILNSPNNPTGRTLSLEELISWVKLALKHDFILINDECYSEIYENTPPPSLLEACMLAGNEAFKNVLVIHSLSKRSSAPGLRSGFIAGDSRLLEKYKAFRAYLGYTSANAIQKASEAAWLDDRHAEFFRNIYANNLKLARKIFKNTLIYPYSFYVYLPVQNGENFAKTLYQNEGIITLPALYLGRNRIGADYVRLALVYDTPLLEKPLEIIETYREN 373
               SCOP domains d3ezsa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh....................hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...hhh.eeee..hhhhhhhhhhhhh......eeeeee...hhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhh.eeee...........hhhhhhhhhhhhhhhh.eeeee.............hhhhhhhhh.......eeeeee......hhhhh.eeeeehhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeee..hhhhhhhhhhhhhh...ee.hhhh.......eeeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ezs A   0 GmTFEPYPFERLRALLKEITPKKRGLDLGIGEPQFETPKFIQDALKNHTHSLNIYPKSAFEESLRAAQRGFFKRRFKIELKENELISTLGSREVLFNFPSFVLFDYQNPTIAYPNPFYQIYEGAAKFIKAKSLLmPLTKENDFTPSLNEKELQEVDLVILNSPNNPTGRTLSLEELISWVKLALKHDFILINDECYSEIYENTPPPSLLEACmLAGNEAFKNVLVIHSLSKRSSAPGLRSGFIAGDSRLLEKYKAFRAYLGYTSANAIQKASEAAWLDDRHAEFFRNIYANNLKLARKIFKNTLIYPYSFYVYLPVQNGENFAKTLYQNEGIITLPALYLGRNRIGADYVRLALVYDTPLLEKPLEIIETYREN 373
                             |       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    
                             |                                                                                                                                  134-MSE                                                                       212-MSE                                                                                                                                                             
                             1-MSE                                                                                                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:374
 aligned with O25341_HELPY | O25341 from UniProtKB/TrEMBL  Length:375

    Alignment length:374
                                    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    
         O25341_HELPY     1 MTFEPYPFERLRALLKEITPKKRGLDLGIGEPQFETPKFIQDALKNHTHSLNIYPKSAFEESLRAAQRGFFKRRFKIELKENELISTLGSREVLFNFPSFVLFDYQNPTIAYPNPFYQIYEGAAKFIKAKSLLMPLTKENDFTPSLNEKELQEVDLVILNSPNNPTGRTLSLEELISWVKLALKHDFILINDECYSEIYENTPPPSLLEACMLAGNEAFKNVLVIHSLSKRSSAPGLRSGFIAGDSRLLEKYKAFRAYLGYTSANAIQKASEAAWLDDRHAEFFRNIYANNLKLARKIFKNTLIYPYSFYVYLPVQNGENFAKTLYQNEGIITLPALYLGRNRIGADYVRLALVYDTPLLEKPLEIIETYRENH 374
               SCOP domains d3ezsb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh....................hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...hhh.eeee..hhhhhhhhhhhhh......eeeeee...hhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhh.eeee...........hhhhhhhhhhhhhhh..eeeee.............hhhhhhhhh.......eeeeeehhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeee..hhhhhhhhhhhhhh...ee.hhhh.......eeeee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ezs B   1 mTFEPYPFERLRALLKEITPKKRGLDLGIGEPQFETPKFIQDALKNHTHSLNIYPKSAFEESLRAAQRGFFKRRFKIELKENELISTLGSREVLFNFPSFVLFDYQNPTIAYPNPFYQIYEGAAKFIKAKSLLmPLTKENDFTPSLNEKELQEVDLVILNSPNNPTGRTLSLEELISWVKLALKHDFILINDECYSEIYENTPPPSLLEACmLAGNEAFKNVLVIHSLSKRSSAPGLRSGFIAGDSRLLEKYKAFRAYLGYTSANAIQKASEAAWLDDRHAEFFRNIYANNLKLARKIFKNTLIYPYSFYVYLPVQNGENFAKTLYQNEGIITLPALYLGRNRIGADYVRLALVYDTPLLEKPLEIIETYRENH 374
                            |       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    
                            1-MSE                                                                                                                              134-MSE                                                                       212-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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O25341_HELPY | O25341)
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:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

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