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(-) Description

Title :  STRUCTURE OF A PYRROLINE-5-CARBOXYLATE REDUCTASE (PROC) FROM COXIELLA BURNETII
 
Authors :  J. Cheung, M. C. Franklin, M. Rudolph, M. Cassidy, E. Gary, F. Burshteyn
Date :  09 Sep 11  (Deposition) - 28 Sep 11  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Amino Acid Biosynthesis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Franklin, J. Cheung, M. J. Rudolph, F. Burshteyn, M. Cassidy, E. Gary, B. Hillerich, Z. K. Yao, P. R. Carlier, M. Totrov, J. D. Love
Structural Genomics For Drug Design Against The Pathogen Coxiella Burnetii.
Proteins V. 83 2124 2015
PubMed-ID: 26033498  |  Reference-DOI: 10.1002/PROT.24841

(-) Compounds

Molecule 1 - PYRROLINE-5-CARBOXYLATE REDUCTASE
    Chains: A, B
    EC Number: 1.5.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CBU_2090, PROC
    Organism Scientific: COXIELLA BURNETII
    Organism Taxid: 777

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric/Biological Unit (4, 19)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MSE12Mod. Amino AcidSELENOMETHIONINE
3NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4PO44Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , GLY A:12 , ASN A:13 , MSE A:14 , ASN A:36 , ARG A:37 , SER A:38 , LYS A:41 , ASN A:57 , ALA A:70 , VAL A:71 , LYS A:72 , PRO A:73 , GLN A:75 , MSE A:78 , LEU A:97 , ALA A:98 , VAL A:99 , MSE A:120 , PRO A:121 , HOH A:293 , HOH A:294 , PHE B:230 , VAL B:231 , PO4 B:283BINDING SITE FOR RESIDUE NAP A 281
2AC2SOFTWAREALA A:217 , LEU A:218 , THR A:220 , GLU A:221 , GLN A:222 , GLU B:207BINDING SITE FOR RESIDUE PO4 A 282
3AC3SOFTWAREASN A:5 , ILE A:6 , THR A:7 , ARG A:31 , ILE A:32 , CYS A:33 , GLY A:60 , ASN A:63 , ALA A:64BINDING SITE FOR RESIDUE PO4 A 283
4AC4SOFTWARESER A:150 , GLU A:190 , GLU A:193 , GLN A:194BINDING SITE FOR RESIDUE PO4 A 284
5AC5SOFTWAREGLY B:10 , GLY B:12 , ASN B:13 , MSE B:14 , ASN B:36 , ARG B:37 , SER B:38 , LYS B:41 , ASN B:57 , ALA B:70 , VAL B:71 , LYS B:72 , PRO B:73 , GLN B:75 , LEU B:97 , VAL B:99 , PRO B:121 , HOH B:309BINDING SITE FOR RESIDUE NAP B 281
6AC6SOFTWAREASP B:28 , ARG B:37BINDING SITE FOR RESIDUE CL B 282
7AC7SOFTWAREVAL A:99 , NAP A:281 , SER B:233 , THR B:237 , HOH B:332BINDING SITE FOR RESIDUE PO4 B 283

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TRI)

(-) 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:272
 aligned with Q83A21_COXBU | Q83A21 from UniProtKB/TrEMBL  Length:274

    Alignment length:272
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271  
         Q83A21_COXBU     2 NTSNITFIGGGNMARNIVVGLIANGYDPNRICVTNRSLDKLDFFKEKCGVHTTQDNRQGALNADVVVLAVKPHQIKMVCEELKDILSETKILVISLAVGVTTPLIEKWLGKASRIVRAMPNTPSSVRAGATGLFANETVDKDQKNLAESIMRAVGLVIWVSSEDQIEKIAALSGSGPAYIFLIMEALQEAAEQLGLTKETAELLTEQTVLGAARMALETEQSVVQLRQFVTSPGGTTEQAIKVLESGNLRELFIKALTAAVNRAKELSKTVD 273
               SCOP domains d3tria1 A:2-162 automated matches                                                                                                                                d3tria2 A:163-273 automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhh..hhh.eeee...hhhhhhhhhh...eee.hhhhhhh...eeee..hhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhh....eeeee.hhhhhhh.eeeeee.....hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tri A   2 NTSNITFIGGGNmARNIVVGLIANGYDPNRICVTNRSLDKLDFFKEKCGVHTTQDNRQGALNADVVVLAVKPHQIKmVCEELKDILSETKILVISLAVGVTTPLIEKWLGKASRIVRAmPNTPSSVRAGATGLFANETVDKDQKNLAESImRAVGLVIWVSSEDQIEKIAALSGSGPAYIFLImEALQEAAEQLGLTKETAELLTEQTVLGAARmALETEQSVVQLRQFVTSPGGTTEQAIKVLESGNLRELFIKALTAAVNRAKELSKTVD 273
                                    11  |     21        31        41        51        61        71      | 81        91       101       111       121       131       141       151|      161       171       181   |   191       201       211    |  221       231       241       251       261       271  
                                       14-MSE                                                          78-MSE                                   120-MSE                         152-MSE                          185-MSE                        216-MSE                                                     


Chain B from PDB  Type:PROTEIN  Length:270
 aligned with Q83A21_COXBU | Q83A21 from UniProtKB/TrEMBL  Length:274

    Alignment length:270
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271
         Q83A21_COXBU     2 NTSNITFIGGGNMARNIVVGLIANGYDPNRICVTNRSLDKLDFFKEKCGVHTTQDNRQGALNADVVVLAVKPHQIKMVCEELKDILSETKILVISLAVGVTTPLIEKWLGKASRIVRAMPNTPSSVRAGATGLFANETVDKDQKNLAESIMRAVGLVIWVSSEDQIEKIAALSGSGPAYIFLIMEALQEAAEQLGLTKETAELLTEQTVLGAARMALETEQSVVQLRQFVTSPGGTTEQAIKVLESGNLRELFIKALTAAVNRAKELSKT 271
               SCOP domains d3trib1 B:2-162 automated matches                                                                                                                                d3trib2 B:163-271 automated matches                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhh..hhh.eeee..hhhhhhhhhhh...eee.hhhhhhh...eeee..hhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhh...eeeeee.hhhhhhh.eeeeeee....hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tri B   2 NTSNITFIGGGNmARNIVVGLIANGYDPNRICVTNRSLDKLDFFKEKCGVHTTQDNRQGALNADVVVLAVKPHQIKmVCEELKDILSETKILVISLAVGVTTPLIEKWLGKASRIVRAmPNTPSSVRAGATGLFANETVDKDQKNLAESImRAVGLVIWVSSEDQIEKIAALSGSGPAYIFLImEALQEAAEQLGLTKETAELLTEQTVLGAARmALETEQSVVQLRQFVTSPGGTTEQAIKVLESGNLRELFIKALTAAVNRAKELSKT 271
                                    11  |     21        31        41        51        61        71      | 81        91       101       111       121       131       141       151|      161       171       181   |   191       201       211    |  221       231       241       251       261       271
                                       14-MSE                                                          78-MSE                                   120-MSE                         152-MSE                          185-MSE                        216-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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q83A21_COXBU | Q83A21)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004735    pyrroline-5-carboxylate reductase activity    Catalysis of the reaction: L-proline + NADP+ = 1-pyrroline-5-carboxylate + NADPH + H+.
biological process
    GO:0055129    L-proline biosynthetic process    The chemical reactions and pathways resulting in the formation of L-proline, an L-enantiomer of a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    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.
    GO:0006561    proline biosynthetic process    The chemical reactions and pathways resulting in the formation of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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