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(-) Description

Title :  CRYSTAL STRUCTURE OF CELL SHAPE DETERMINANT PROTEIN CSD4 GLN46HIS VARIANT FROM HELICOBACTER PYLORI
 
Authors :  A. C. Chan, M. E. Murphy
Date :  05 Sep 14  (Deposition) - 24 Dec 14  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Mixed Alpha Beta Sandwich, Carboxypeptidase, M14, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. C. Chan, K. M. Blair, Y. Liu, E. Frirdich, E. C. Gaynor, M. E. Tanner, N. R. Salama, M. E. Murphy
Helical Shape Of Helicobacter Pylori Requires An Atypical Glutamine As A Zinc Ligand In The Carboxypeptidase Csd4.
J. Biol. Chem. V. 290 3622 2015
PubMed-ID: 25505267  |  Reference-DOI: 10.1074/JBC.M114.624734

(-) Compounds

Molecule 1 - CONSERVED HYPOTHETICAL SECRETED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B(MOD)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HPG27_353
    Mutation: YES
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 563041
    Strain: G27

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 43)

Asymmetric/Biological Unit (4, 43)
No.NameCountTypeFull Name
1API1Ligand/Ion2,6-DIAMINOPIMELIC ACID
2IOD37Ligand/IonIODIDE ION
3PO41Ligand/IonPHOSPHATE ION
4ZN4Ligand/IonZINC ION

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:319binding site for residue IOD A 502
02AC2SOFTWAREASN A:267binding site for residue IOD A 504
03AC3SOFTWAREASN A:84 , LYS A:325 , HOH A:927binding site for residue IOD A 506
04AC4SOFTWAREPRO A:136binding site for residue IOD A 507
05AC5SOFTWAREHIS A:38binding site for residue IOD A 509
06AC6SOFTWARELYS A:163 , HOH A:926binding site for residue IOD A 510
07AC7SOFTWARETHR A:400 , HOH A:982binding site for residue IOD A 511
08AC8SOFTWAREPHE A:341binding site for residue IOD A 512
09AC9SOFTWAREHIS A:292binding site for residue IOD A 514
10AD1SOFTWAREASP A:157 , ASN A:193binding site for residue IOD A 515
11AD2SOFTWAREGLN A:156 , LYS A:160binding site for residue IOD A 516
12AD3SOFTWARELYS A:146binding site for residue IOD A 518
13AD4SOFTWARESER A:64 , HOH A:921binding site for residue IOD A 519
14AD5SOFTWARESER A:344binding site for residue IOD A 520
15AD6SOFTWAREARG A:147 , HOH A:819binding site for residue IOD A 521
16AD7SOFTWARELYS A:78binding site for residue IOD A 522
17AD8SOFTWAREGLN A:320 , ZN A:541binding site for residue IOD A 523
18AD9SOFTWAREARG A:147binding site for residue IOD A 524
19AE1SOFTWAREILE A:301 , LYS A:317binding site for residue IOD A 525
20AE2SOFTWAREHOH A:711binding site for residue IOD A 526
21AE3SOFTWAREGLN A:303binding site for residue IOD A 527
22AE4SOFTWAREARG A:83binding site for residue IOD A 528
23AE5SOFTWAREARG A:86binding site for residue IOD A 529
24AE6SOFTWARELYS A:102 , SER A:260binding site for residue IOD A 530
25AE7SOFTWARELYS A:300binding site for residue IOD A 531
26AE8SOFTWAREZN A:541binding site for residue IOD A 533
27AE9SOFTWAREZN A:541binding site for residue IOD A 534
28AF1SOFTWARESER A:387 , GLN A:407binding site for residue IOD A 537
29AF2SOFTWAREHIS A:46 , GLU A:49 , HIS A:128 , PO4 A:542binding site for residue ZN A 538
30AF3SOFTWAREHIS A:62 , ASP A:254 , HOH A:869binding site for residue ZN A 539
31AF4SOFTWAREHIS A:181 , HOH A:979binding site for residue ZN A 540
32AF5SOFTWAREMET A:358 , IOD A:523 , IOD A:533 , IOD A:534binding site for residue ZN A 541
33AF6SOFTWAREHIS A:46 , GLU A:49 , ARG A:86 , HIS A:128 , ASP A:129 , GLU A:222 , ZN A:538 , API A:543 , HOH A:840binding site for residue PO4 A 542
34AF7SOFTWAREHIS A:46 , ASN A:93 , ARG A:94 , HIS A:126 , HIS A:128 , TRP A:148 , MET A:203 , THR A:208 , ALA A:220 , GLU A:222 , PO4 A:542 , HOH A:729binding site for residue API A 543

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WCM)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:426 -Asn A:427

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WCM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WCM)

(-) Exons   (0, 0)

(no "Exon" information available for 4WCM)

(-) 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:415
                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...hhhhhhhh.eeeee......hhhhhhhhhhhhhheee...eeeee...hhhhhhh.......hhhhh.........hhhhhhhhhhhhh.....eeeeeeee..ee........ee......eeee...........hhhhhhhhhhhhhhhhh.hhhhh.eeee.hhhhh..hhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhh....eeee.....ee......eeeeeeee...hhhhh.eee....eeeeee..eeeeee..eeeeeeeeeee.......eeeeee..eeeeee...eeee..eeee......eeee............eee.hhhhhhhh......eeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wcm A  20 MEMIEKAPTDLEDRDKAPHLLLLAGIHGDEPGGFNATNLFLMHYSVLKGLVEVVPVLNKPSMLRNHRGLYGDMNRKFAALDKKDPEYPTIQEIKSLIAKPNIDAVLHLHDGGGYYRPVYVDAMLNPKRWGNCFIIDQDEVKGAKFPNLLAFANNTIESINAHLLHPIEEYHLKNTRTAQGDTEMQKALTFYAINQKKSAFANEASKELPLASRVFYHLQAIEGLLNQLNIPFKRDFELNPSSVHALINDKSLWAKISSLPKIPLFNLRPRLNHFPLPHNTKIPQIPIESNAYIVGLVKNKQEVFLKYGNKLMTRLSPFYIEFDPSLEEVKMQIDNKDQMVKIGSVVEVKESFYIHAMDNIRANVIGFSVKPNEAGYTIRFKDFQKRFSLDKQERIYRIEFYKNNAFSGMILVKFV 438
                                    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       393       403       413       423       433     
                                                                                                                                                                                                                                                                                                                                                                                                          388|                                             
                                                                                                                                                                                                                                                                                                                                                                                                           393
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4WCM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WCM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WCM)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:426 - Asn A:427   [ RasMol ]  
 

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        B5ZAD9_HELPG | B5ZAD9: 4wck 4wcl 4wcn 5d2r

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4wck 4wcl 4wcn